A sex organ (or reproductive organ) is any part of an animal's body that is involved in sexual reproduction. The reproductive organs together constitute the reproductive system. The test is in the male, and the ovary in the female, are called the primary sex organs. All others are called secondary sex organs, divided between the external sex organs the genitals or genitalia, visible at birth in both sexes and the internal sex organs. Mosses, ferns, and some similar plants have gametangia for reproductive organs, which are part of the gametophyte. The flowers of flowering plants produce pollen and egg cells, but the sex organs themselves are inside the gametophytes within the pollen and the ovule. Coniferous plants likewise produce their sexually reproductive structures within the gametophytes contained within the cones and pollen. The cones and pollen are not themselves sexual organs.

In typical prenatal development, sex organs originate from a common primordium during early gestation and differentiate into male or female sexes. The SRY gene, usually located on the Y chromosome and encoding the testis determining factor, determines the direction of this differentiation. The absence of it allows the gonads to continue to develop into ovaries. Thereafter, the development of the internal, and external reproductive organs is determined by hormones produced by certain fetal gonads (ovaries or testes) and the cells' response to them. The initial appearance of the fetal genitalia looks basically feminine: a pair of "urogenital folds" with a small protuberance in the middle, and the urethra behind the protuberance. If the fetus has testes, and if the testes produce testosterone, and if the cells of the genitals respond to the testosterone, the outer urogenital folds swell and fuse in the midline to produce the scrotum; the protuberance grows larger and straighter to form the penis; the inner urogenital swellings grow, wrap around the penis, and fuse in the midline to form the penile urethra.

Each sex organ in one sex has a homologous counterpart in the other one. See a list of homologues of the human reproductive system. In a larger perspective, the whole process of sexual differentiation also includes development of secondary sexual characteristics such as patterns of pubic and facial hair and female breasts that emerge at puberty. Furthermore, differences in brain structure arise, affecting, but not absolutely determining, behavior. Intersex is the development of genitalia somewhere between typical male and female genitalia. Once the child is born, the parents are faced with decisions that are often difficult to make, such as whether or not to modify the genitalia, assign the child as male or female, or leave the genitalia as is. Some parents allow their doctors to choose. If they do decide to modify the genitalia, they have approximately a 50% chance of getting genitalia that will match the child's gender identity. If they pick the wrong one, their child may begin to show symptoms of transsexualism, which can lead them to a life of discomfort until they are able to remedy the issue.

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