The testis are ovoid masses of seminary tubules, interstitial cells and vessels, all encapsulated in a connective tissue. They are located dorso-medial in the coelomic cavity and exact location is species specific. The right testis is located cranially in comparison to the left. Snakes lack an epididymis.

The copulating organ varies amongst groups, presenting as a single organ in crocodilians and chelonians, and a pair of hemipenes in lizards and snakes. There is a canal that passes through the middle-called sulcus spermaticus where sperm is carried and deposited in the female cloaca. 

Ovaries are located in a similar position as the testis and they consist of epithelial cells, connective tissue, nerves, vessels and germinal cells encapsulated by an elastic tunic. The ovarian appearance will be dependent on oogenesis state, presenting as small and granular when inactive, and enlarged and lobular, full of vitellogenic follicles when active.

In chelonia, the existence of glandular crypts located in distal oviducts permit the storage and feeding to spermatozoa, sometimes for years before fertilisation. The phenomenon is called amphigonia retardata and it enables reproduction in females that have a short active period or where a low census exists.

A true uterus in non-existent and the oviducts functions include secretion of albumin and shell.

Reptiles can either be oviparous (egg layers) or viviparous (live bearing) with internal fertilization. Viviparous species may depend entirely on the yolk (previously called ovoviviparous) or a corioalantoid placenta may be present (true viviparism). Maternal contribution of nutrients is achieved through lecithotrophy (feeding from yolk) or mammotrophy (feeding through placenta). The latter may be achieved up to 99% as is the case in some skinks. Newborns are small replicas of adults and some cases include oncogenetic changes (i.e. skin pigmentation in Morelia viridis). 

Viviparous species normally have a phase or anorexia during the latter stage of pregnancy; oviparous species may also but for a shorter period of time.

Sexual maturity is determined mainly by size, although age is important also. The age of onset found in the literature often is referring to wild animals, although there are species frequently kept in captivity for which we may find data.

Factors including diet and general care may vary the onset of sexual maturity. We are able to find specimens of snakes that have reached 2 metres over 18 months and others are hardly 1 metre in length after 10 years.

As a general guide or reference we may consider the following for animals kept in optimal conditions: snakes 2-3 years, small lizards 1-2 years, larger lizards 3-4 years and chelonia 5-7 years.

It is though that most vertebrates respond to environmental stimulus so that the offspring may encounter favorable conditions for survival (Mayr 1974; Pianka 1976; Williams 1966).

Reproductive seasons are synchronised so that clutches or births happen around the most favorable time of year. Species from temperate zones will hatch or are born in the spring/summer, coinciding with ideal climate conditions. In tropical climates, births or hatchings occur during the humid season when prey is abundant. Reproductive capacity in mature females is dependent on the fat cycle which is dependent on food availability. Once a female has stored enough fat, changes in temperature, photoperiod or humidity will stimulate the release of reproductive neuropeptides.

The reproductive season for most species starts in the spring after a season of cooler temperatures. There are exceptions though, for example in Boa Constrictors and Burmese Pythons that start their behavioural changes during the cooler season.

Probably the two most important factors in temperate climates are photoperiod and temperature. It has been known for many years that temperature is a determining factor in these climates (Whittier and Crews, 1987). Food availability is also another important factor, as is inter and intra-specific interactions and even light intensity.

The relation between hypophyseal gonadotropins and secretion of gonadal sexual steroids during the reproductive season has been widely studied (Whittier and Crews, 1987; Whittier et al., 1987; Whittier and Tokarz, 1992).

Studies on lizards in tropical climates have proven that actually there is little relation between environmental conditions and breeding season (Shine 1985; James and Shine 1985; Auffenberg and Auffenberg 1989; Vitt 1990).

Predictions based on studies that linked the breeding season with rainfalls seemed to be incorrect (Fitch, 1982). A study involving over 3000 tropical lizards found a huge reproductive strategical diversity with diverse factors that influenced breeding cycles. Albeit, the study included different species within the same family and many within the same microhabitat. There were one and two year reproductive cycles, lasting all year round or without a clear link to a season (Auffenberg, 1989). This just goes to prove how complex reproduction can be in different species. There are species of lizards found in the Philippines, Tropical America and Australia that breed during the wet season, all year round and at any time of year.

Successful reproduction is the result of a series of internal and external interactions and cues. External factors include climate, physical and social factors, whereas internal factors include genetic and hormonal factors.

External factors include temperature (environmental), photoperiod, light intensity, interspecific interactions, humidity, rainfall, Nutrition and availability of food.

Is been proven in some species that temperature is extremely important and photoperiod does not affect reproduction at all. This was the case in Thamnophis sirtalis parietalis (Whittier et al., 1987). In this species, they proved that females are maintained at low temperatures during a period of 7 to 17 weeks had ovarian activity (vitello-genesis), whereas if they were kept for less time there was no activity.

It is thought that temperature is the most important stimulus for breeding reptiles (Licht, 1972, 1984). It has not been established if temperature is a dominant factor in Chelonia. Previously it was thought that light was less important than temperature in the regulation of the reproductive cycle (Bentley, 1998). It has been proven that there are circa diurnal and circannual fluctuations of serotonin and melatonin in Testudo hermanni and their maximum concentration higher during the breeding season (Vivien-Roels et al., 1979). It seems that temperature and life cycles can influence folliculogenesis and that neither one has absolute control (McArthur, 2004). A male influence at the start of the reproductive cycle has not been determined but it is known that the Green Iguana (parthenogenic species) can progress through the entire oogenic cycle without a male and some species of snakes require the presence of male and possibly copulation to proceed with follicular pre-vitellogenic growth.

Many reptiles, especially snakes, depend on their body reserves to be able to carry out a reproductive cycle and don't depend on food ingestion.

Internal factors consist on the pineal system and the. Through complex systems of interactions and negative feedbacks, these two systems Control reproduction. The pineal system consists of the pineal organ, Formed by photosensitive cells and, In some species what some call the third eye or pineal eye. It is known that these two organs Control the endocrine function circadian rhythms and thermoregulation.

The hypothalamic-hypophyseal-gonadal axis contains hypothalamic, hypophyseal and gonadal neuropeptides very similar to those found in mammals. Changes in temperature, humidity and/or photoperiod stimulate hypothalamic factors that activate the axis. Pituitary or hypophyseal hormones and gonadal hormones initiates copulation behaviour, fertilization, pregnancy and laying or hatching of eggs.

The pituitary gland, ovaries and testicles intervene in reproductive endocrinology in a similar way as in mammals.

Following ovulation, a corpa luthea is formed similar to that found in mammals and studies suggest that progesterone is secreted (Bentley, 1998; Kutchling, 1999). In Chrysemys picta it was found that progesterone inhibits ovulation completely and it also produces decrease in the size of the pituitary gland, oviduct's and follicular size (Klicka and Mahmoud, 1977). It has also been suggested that estrogens and progesterone can influence the release of hypothalamic gonadotropins similar to mammals. It has also been suggested that these may influence clutch size and maintaining pregnancy (Klicka and Mahmoud, 1977). It has also been suggested that vitellogenesis may be inhibited (Callard et al., 1972) in Sceloporus cyanogenys. It is thought that post ovulation levels of progesterone are different depending on the species and in Chelonia mydas progesterone levels were not maintained after ovulation as initially thought (Licht, 1984).

Oestrogens stimulate vitellogenesis, production of lipophosphoproteins by the liver and the incorporation to the egg (Callard et al., 1972; Licht, 1979; Duval et al., 1982; Kutchling, 1999).

Increased testosterone levels have been registered during the population season, straight after ovulation and it has been related two female receptiveness (Rostal et al., 1998).

Follicular stimulating hormone (FSH) and luteinizing hormone have been identified in reptiles, as has an estrogen Negative feedback on gonadotropin release at pituitary level (Bentley, 1998). It seems that ovarian development and release of testosterone and estrogens are controlled by follicular stimulating hormone (FSH) or non-specific gonadotropins.

Follicle stimulating hormone (FSH) stimulates folliculogenesis and oestradiol production, which initiates vitellogenesis and sexual activity. In response to oestradiol, the liver forms vitellogens which are the substances that are transported to the ovaries where pre-ovulatory formation of yolk is initiated. Pheromone production is also stimulated by oestradiol.

Pheromones released by the females are captured by males via the tongue and transported to the vomeronasal or Jacobson organ. These pheromones stimulate areas in the brain that stimulate copulation. Examples of these glands that release pheromones are femoral or preanal glands in lizards, urodeum glands in skinks or axillary or inguinal glands in chelonians or crocodilians.

Vitellogenesis is an important phase in follicle maturity. Oestrogens stimulate the liver to convert lipid reserves to vitellogenin. The liver increases in size and has a yellow appearance. Vitellogenin is absorbed from the blood circulation by the follicles. In most reptiles calcium is absorbed through the yolk and blood levels are elevated during this phase. Once ovulation has occurred there is little nutritional exchange between the female and the egg.

In chelonia, two types of vitellogenesis have been described. In the first type, vitellogenesis and follicular growth initiate at the end of summer or autumn and are completed just prior to hibernation in the winter; the second type occurs in tropical regions in reptiles that don’t hibernate. In this type, follicular growth is slow and continuous but doesn’t complete until just before ovulation in the spring (Licht 1984; Duval et al., 1982). Some species, like Chrysemys picta will have one type of vitellogenesis or another depending on geographics (Moll, 1979).

During ovulation, mature follicles are released in the coelomic cavity in to the ostium, which is a structure that directs the follicles to the oviducts where fertilisation occurs. In chelonia this may be induced by the presence of a male. This may be induced by pheromones, male behaviour which may include biting, pushing against the shell or mating (McArthur, 2000; McArthur, 2004).

An egg is formed when albumin and shell is added in the oviduct. The level of calcification varies between species, being flexible in snakes, most lizards and some aquatic turtles, and rigid in crocodilians, tortoises and many geckos.

In lizards such as Green Iguanas and Bearded Dragons follicular development can be monitored via ultrasound. In those cases where pre-ovulatory folliculostasis is suspected, supportive care and ultrasound scans for 2-3 weeks can be performed, which is the time it should take for these to be reabsorbed (Redrobe, personal communication 2012).

Ultrasonography is the diagnostic tool to differentiate between inactive gonads, early pre-vitellogenic growth of follicles, vitello-genesis, ovulation and foetal or shell development. These are usually laid one week after the yolk has been used up.

In oviparous reptiles, the egg shell is produced in the distal part of the oviduct where the egg glands are located. 

Corpa lutea (post-ovulatory follicles) are what maintain the pregnancy or gestational state through progesterone mainly. In chameleons, the colour change is also due to progesterone.

At the end of the pregnancy progesterone levels drop and vasotocin starts uterine contractions. Each oviduct end in the urogenital papilla located dorsally in the urodeum.

In males, sperm is transported from the testicles to the urodeum via the vas deferens, ending in the urogenital papilla.

It is common that males become anorectic during breeding season and/or if kept together with the female. Many males will stop eating form months. This kind of behaviour has been described in Bitis, Boa, Bothriechis, Bothrops, Chondropython, corallus, Crotalus, Dispholidus, Elaphe, Epicrates, Eryx, Lampropeltis, Lamprophis, Liasis, Python and Senticolis (Boyer and Boyer, 1993). Some of the most extreme cases are probably Corrallus caninus, with periods of anorexia extending to 5-9 months, and Lamprophis fuliginosus, which have been known to starve if not separated from the females. Liasis fuscus is capable of losing 17% of weight over a six-week period without consequences of detrimental health. It is known that boids and crotalids possess a physiological adaptation to periods of anorexia based on the fact that they can wait for passing food, (Secor and Diamond, 2000). During these periods of anorexia, the intestinal tracts are virtually inactive, and therefore the standard metabolic rate is lower than in other species (Galvao et al., 1965).

Physiological and pathological anorexia may be different to tell the difference. In boas and pythons, a weight loss is considered as in follows: >20% in females and >15%. In other species, a weight loss if 15%-20%.

In lizards, Varanus albigularus albigularis can spend 7 months of anorexia during the dry season (Sector and Philips, 1997).

There are two main factors that determine sex in reptiles: genetics and temperature. The genetic factor depends on sexual chromosomes and temperature plays a major role in chelonia, crocodilians and some species of geckos.