The cause of hypogonadism may be "primary" or "central." In primary hypogonadism, the ovaries or testes themselves do not function properly. Some causes include surgery; radiation; genetic and developmental disorders; liver and kidney disease; infection; and certain auto-immune disorders. The most common genetic disorders are Turner syndrome (in women) and Klinefelter syndrome (in men).

In central hypogonadism, the centers in the brain that control the gonads (hypothalamus and pituitary) do not function properly. Some causes of central hypogonadism include tumors (growths); surgery and radiation; infections; trauma; bleeding; genetic problems; nutritional deficiencies; and iron excess (hemochromatosis).

A genetic cause of central hypogonadism which also produces an inability to smell is Kallmann syndrome (males). The most common tumors affecting the pituitary area are craniopharyngioma (children) and prolactinoma (adults, this leads to the production of excess prolactin (which causes the breasts to produce milk, among other functions). Prolactinomas cause hypogonadism even if they are not large.