The condition is congenital but some forms can be acquired later in life, mainly in females.
The exact genetic cause is unknown, with over 25 different gene / alleles having been found to cause cases of Kallmann syndrome.
The root cause is the failure of the hypothalamus gland to release GnRH in order for the pituitary gland to release the hormones LH and FSH correctly. It is the absence of LH and FSH that cause the infertility and lack of puberty.
The hypothalamus can failure to release GnRH either because it lacks the correct nerve cells to do so or the timing mechanism does not work correctly which means that the GnRH is not released in the correct way for the pituitary gland to be able to respond.