Primary amenorrhoea (PA) is one of the common reproductive disorder affecting females.PA is characterised by the absence of menarche in the reproductive age group in females and some cases with absence of reproductive organs. The study was carried out in large cohort (N=490) of subjects with PA to identify genetic, anatomical and hormonal factors responsible for PA. Conventional cytogenetic and FISH (fluorescence in situ hybridization) technique were applied to detect the chromosomal abnormalities. The chromosomal abnormalities were detected in total 121 (24.7%) females. In our cohort numerical chromosomal aberrations frequency was found to be high (43.8%) as compared to structural abnormalities (26.4%). The 46, XY karyotype was identified in 29.8% patients. The anatomical abnormalities including absences of ovaries (51.2%), streak ovaries (35.6%), hypoplastic uterus (59.6%), absent uterus (22.3%) were also detected and correlated with genetic abnormalities in this cohort. FSH (follicular stimulating hormone) level were also found to be high in these patients. Our study suggests that genetic investigation are important for further management of the disease.