In considering the development of reproductive organs, distinctions must be made between: (1) the origin of sex cells (gametes), (2) the origin and differentiation of the sex glands, or gonads (ovaries and testes), and (3) the origin and development of the supporting parts of the reproductive system (e.g., genital ducts, copulatory organs).

The germ (germinal) cells, which eventually give rise to the gametes, are often segregated from the somatic, or body, cells at a very early stage—during cleavage and before the subdivision of the embryo into ectoderm, mesoderm, and endoderm. In the invertebrate nematodes, the very first of these primordial germ cells is identifiable after as few as five divisions of the egg cell. The germ cell retains the large chromosomes present in the fertilized egg; in the somatic cells the chromosomes become fragmented. Subsequently, the single germ cell gives rise, by mitotic divisions, to all the gametes in the gonad.

In vertebrates, primordial germ cells arise outside the gonads, but they cannot be distinguished in early cleavage stages. In amphibians, cytoplasm at the vegetal pole, rich in ribonucleic acids, becomes incorporated into a number of cells, which, during cleavage and gastrulation, lie among the yolky endoderm cells. Later they migrate into the mesodermal layer and become incorporated into the rudiments of the gonads. In higher vertebrates, primordial germ cells can be recognized in the extra-embryonic endoderm of the yolk sac. In mammals, these cells subsequently migrate into the mesoderm and are located in the gonad rudiments. The mouse embryo, for example, originally has fewer than 100 primary germ cells; during their migration, however, their numbers increase as a result of repeated divisions, to 5,000 or more in the gonads.

Although the primordial germ cells either may appear before the separation of germinal layers or be found originally in the endoderm, the gonads are invariably of mesodermal origin. In vertebrates, the first trace of gonad development is a thickening of the coelomic lining on either side of the dorsal mesentery and medial to the kidney rudiments. The thickening, elongated anteroposteriorly, is known as the germinal ridge. The ridge protrudes into the coelomic cavity, and the fold of thickened epithelium becomes filled with mesenchyme. At this stage the primordial germ cells invade the rudiments of the gonads and become associated with the somatic cells of the germinal ridge. In the functionally differentiated gonads, only the actual gametes and their predecessors (spermatogonia and oogonia) are derived from the primary germ cells; the supporting cells are somatic cells of local mesodermal origin. In the ovaries, the follicle cells surrounding and nourishing the young egg cells (oocytes) are of somatic origin, as are also the connective tissue and blood vessels of the gonad. In the testes, supporting elements called Sertoli cells are somatic cells, as are the interstitial cells, which are scattered between the sperm-carrying tubules of the testes and believed to be the source of male hormones.

In the early stages of their development—even while the gonad rudiment is being invaded by primordial germ cells—the female and male gonads are in an indifferent stage. Only later does tissue differentiation of the gonads begin and male or female gonadal development proceed.

The genital ducts, by which the eggs and sperm are carried away from the gonads, are, in vertebrates, linked with the excretory system. In the male, the seminiferous tubules connect with the nephric tubules of the mesonephros, and the sperm are carried to the exterior by way of the mesonephric duct. In males of lower vertebrates, the mesonephric duct thus serves as a channel both for urine and for sex cells. In amniotes the development of the metanephros as the urine excreting organ has freed the mesonephric duct to carry products associated only with reproduction. In the female, a separate duct, the paramesonephric duct (Müllerian duct), develops beside the mesonephric duct. At its anterior end it utilizes the funnels of the pronephric tubules as its entrance (ostium). The paramesonephric duct develops initially in both female and male embryos. The ducts remain in an indifferent stage longer than the gonads. Eventually the sex hormones produced by the differentiating gonads cause a corresponding differentiation of the ducts. The mesonephric ducts, which become reduced in female embryos, remain in male embryos as ducts for conveying sperm (ductus deferens). The paramesonephric ducts, on the other hand, degenerate in male embryos but become the oviducts in female embryos. In mammals, the terminal portions of the paired oviducts differentiate as two uteri, which, in primates and man, fuse to form a single uterus.

In all terrestrial vertebrates except the placental mammals, the genital ducts, as well as the ducts of excretory organs, open into the cloaca. In mammals, however, the cloaca becomes subdivided into a dorsal part, which conveys the feces, and a ventral part, which receives excretory and genital products. In male mammals the excretory and genital ducts remain connected, having the urethra as their common outlet; in females the urethra serves only for the passage of urine and the uterus opens separately by means of the vagina. In nearly all vertebrates, the male nephric duct is utilized in some degree for the conduction of sperm.

Copulatory organs have developed independently in several groups of vertebrates having internal fertilization. The penis in mammals develops from an outgrowth called the genital tubercle, located at the anterior edge of the urinogenital orifice. The tubercle is laid down in a similar way in embryos of both sexes, and the region of the urinogenital orifice remains in an indifferent state even longer than do the genital ducts. In a comparatively late stage of embryonic life the genital tubercle of male embryos encloses the urethral canal and becomes the penis; in female embryos it remains small and becomes the clitoris.

The alimentary canal

The alimentary canal is the chief organ developing from endoderm. The way it forms depends on the type of egg cleavage. In eggs with holoblastic (complete) cleavage, after gastrulation the invaginated mass of endoderm lines the archenteron, the cavity of which becomes the alimentary canal, or gut. In eggs with meroblastic (partial) cleavage—and also in mammals (despite their complete cleavage)—the endoderm is produced in the form of a sheet lying flat over the yolk-sac cavity. Subsequently, folds of endoderm and splanchnic mesoderm appear—first anteriorly, then laterally, and lastly posteriorly—and sink, converging ventrally under the embryo and cutting off the future gut cavity from the cavity of the yolk sac. The most anterior and posterior portions of the gut separate, but the middle part remains in open communication with the yolk sac throughout embryonic life, eventually becoming reduced to the yolk stalk, which passes through the umbilical cord.

The alimentary canal of vertebrates becomes differentiated into the oral cavity, pharynx, esophagus, stomach, and intestine. Whether derived from an archenteron or formed by folding of the endodermal sheet, the canal initially does not possess an opening at its anterior end. This is also the case in some lower chordates and echinoderms, which are grouped together with vertebrates as the Deuterostomia, or animals with secondary mouths.

In vertebrates, a mouth forms by a rupture at the anterior end, where the endoderm is in contact with ectoderm. The ectoderm of the future mouth region becomes depressed, forming a mouth invagination, or stomodaeum. The ectodermal and endodermal layers separating the cavity of the stomodaeum from the gut fuse to form the oropharyngeal membrane, which thins and ruptures, providing free passage from the exterior to the gut. Because of its mode of origin, the oral cavity is in part lined by ectoderm and in part by endoderm, the two parts becoming indistinguishable. Before the oropharyngeal membrane ruptures, however, a small pocket forms on the dorsal side of the stomodaeal invagination. This, the rudiment of the anterior lobe of the hypophysis, becomes apposed to the ventral surface of the diencephalon and loses its connection with the mouth cavity.

The anal opening in some exceptional cases (urodele amphibians) is derived directly from the blastopore, which persists as a narrow canal after completion of gastrulation. In other vertebrates, however, the anus develops either near the location of the former blastopore or in a corresponding region at the posterior end of the embryo, where the last remnants of mesoderm migrated to the interior. It is thus claimed that the anus in vertebrates is derived, directly or indirectly, from the blastopore. The mode of formation of the opening is somewhat similar to that of the mouth. A slight invagination of the ectoderm occurs, and a cloacal membrane forms, separating the ectodermal invagination from the gut cavity. The membrane ruptures later to provide the anus.