Kallmann syndrome is characterized by:

• Hypogonadotropic hypogonadism (a lack of the pituitary hormones LH and FSH)
• Congenital (present from birth) anosmia (complete inability to smell) or hyposmia (decreased ability to smell)

It can occasionally be associated with optic problems, such as colour blindness or optic atrophy, nerve deafness, cleft palate, cryptorchidism, renal agenesis, and mirror movement disorder. However, it is not clear at this time how or if these other problems have the same cause as the hypogonadism and anosmia. These problems are more often present in those without Kallmann syndrome.

Males present with delayed puberty and may have micropenis (although congenital micropenis is not present in the majority of male KS cases). Females present with delayed puberty (i.e. primary amenorrhea) and lack of secondary sex characteristics, such as breast development.