The hypothalamus controls some of the basic functions of life including hormonal activity via the pituitary gland. There are several gender differences in the gland present between males and females.

Some of the differences between male and female hypothalamus can be listed as:

• The volume of a specific nucleus in the hypothalamus (third cell group of the interstitial nuclei of the anterior hypothalamus) is twice as large in heterosexual men as in women and homosexual men
• In addition, the preoptic area that regulates mating behavior, is about 2.2 times larger in men than in women and contains 2 times more cells. This large size depends on the amount of male sex hormones or androgens. The difference in this area is only apparent after a child is 4 years old. In girls at 4 years of age there is a decrease in the number of cells in this nucleus.
• The shape of the suprachiasmatic nucleus of the hypothalamus, involved with circadian rhythms and reproduction cycles is different in men and women. In males, this nucleus is shaped like a sphere whereas in females it is more elongated. The volume is similar. The difference in shape may be due to different connections.
• In men, the hypothalamus has a higher number of androgen receptors (AR) than young adult women. There are differences in ARs in horizontal diagonal band of Broca, the sexually dimorphic nucleus of the preoptic area, the medial preoptic area, the dorsal and ventral zone of the periventricular nucleus, the paraventricular nucleus, the supraoptic nucleus, the ventromedial hypothalamic nucleus and the infundibular nucleus
• Males and females respond differently to ovarian steroids due to differences in estrogen receptor status.
• The mamillary body complex is known to receive input from the hippocampus by the fornix. It is involved in cognitive skills. This is different in the two sexes.
• The differences bring about several functional differences between males and females. For instance, males in most of the species of animals prefer the odor and appearance of females over males. If the sexually dimorphic nucleus of the hypothalamus is damaged, this preference for females by males diminishes.