The commonest cause of primary Amenorrhoea is:
Genital tuberculosis
Ovarian dysgenesis
Mullerian duct anomalies
Hypothyroidism
Most common cause of Primary Amenorrhea = Gonadal dysgenesis/ovarian dysgenesis
2nd most common cause of Primary Amenorrhea = Mullerian agenesis (Mayer Rokitansky Kuster Hauser Syndrome) 

“Mullerian agenesis is a relatively common cause of primary amenorrhea, more frequent than congenital androgen insensitivity and second only to gonadal dysgenesis”

 3rd most common cause is testicular feminizing syndrome.