The commonest cause of primary Amenorrhoea is:
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.
Genital tuberculosis
Ovarian dysgenesis
Mullerian duct anomalies
Hypothyroidism