Even though the etiology of primary amenorrhea and secondary amenorrhea overlap to a great extent, it is prudent to discuss secondary amenorrhea separately. Conditions like testicular feminization syndrome or MRKH exclusively present as primary amenorrhea. Certain conditions present either as primary or secondary amenorrhea. The typical examples are mosaic turner syndrome and HPO dysfunction .The acquired diseases of genital tract like Asherman syndrome, autoimmune premature ovarian failure and tumors of the pituitary or hypothalamus usually present as secondary amenorrhea. When these acquired disorders occur in a girl before puberty, she can present as primary amenorrhea. This chapter describes a protocol for arriving at the organ system responsible for causing amenorrhea. Once the diagnosis is arrived at, management can be planned.