The major sex hormones are testosterone, which is produced in the male by the testes, and estrogen and progesterone, which are produced in the female by the ovaries. Levels of the sex hormones are regulated by two hormones secreted by the pituitary: FSH (follicle-stimulating hormone) and LH (luteinizing hormone). The gonads, pituitary, and hypothalamus regulate one another's output through a negative feedback loop. Inhibin regulates FSH levels.

At conception males and females differ only in the sex chromosomes (XX in females and XY in males). As the male fetus grows, the SRY gene on the Y chromosome directs the gonads to differentiate into the testes. In the absence of the SRY gene, ovaries develop. Different hormones are then produced by the gonads, and these stimulate further differentiation of the internal and external reproductive structures of males and females. A male organ and a female organ that derive from the same embryonic tissue are said to be homologous to each other.

Intersex conditions are generally the result of various syndromes (such as CAH) and accidents that occur during the course of prenatal sexual differentiation. Currently there is a debate over the best medical treatment of these individuals. The Guevodoces provide an interesting case of gender change at puberty.

Puberty is initiated and characterized by a great increase in the production of sex hormones. Pubertal changes in both males and females include body growth, the development of pubic and axillary hair, and increased output from the oil-producing glands. Changes in the female include breast development and the beginning of menstruation. Changes in the male include growth of the penis and testes, the beginning of ejaculation, and a deepening of the voice.

Biologically, the menstrual cycle is divided into four phases: the follicular phase, ovulation, the luteal phase, and menstruation. Corresponding to these phases, there are changes in the levels of pituitary hormones (FSH and LH) and in the levels of ovarian hormones (estrogen and progesterone), as well as changes in the ovaries and the uterus. A fairly common menstrual problem is dysmenorrhea, or painful menstruation.

Research indicates that some, though not all, women experience changes in mood over the phases of the menstrual cycle. For those who experience such changes, their mood is generally positive around the middle of the cycle (around ovulation), and negative moods characterized by depression and irritability are more likely just before and during menstruation. These negative moods and physical discomforts are termed the premenstrual syndrome (PMS). However, research indicates that there are no fluctuations in performance over the cycle. Some evidence suggests that fluctuations in mood are related to changes in hormone levels, but data also suggest that mood fluctuations are related to cultural factors. Research attempting to document whether men experience monthly biological and/or psychological cycles is now in progress.