Objective To analyze the relationship between karyotypes and clinic features of patients with primary amenorrhea. Methods G banding was done for 340 patients with primary amenorrhea to facilitate individual chromosome identification, and if specific staining for certain portions of the chromosome was necessary, C banding was used. The clinical data were recorded by physical examination and ultrasound scanning. Results Karyotype analysis of the 340 patients revealed that 180 (52.94%) patients had normal female karyotypes and 160 (47.06%) patients had abnormal karyotypes. The abnormal karyotypes included abnormal X chromosome (150 patients), mosaic X-Y chromosome (4 patients), abnormal autosome (5 patients), and X-autosome translocation (1 patient). The main clinical manifestations in patients with primary amenorrhea were primordial or absent uterus (95.9%), invisible secondary sex features (68.8%), little or absent ovary (62.6%), and short stature (30.0%). The incidence of short stature in patients with X chromosome aberration (46%, 69/150) was significangly higher that in patients with 46, XX (9.44%, 17/180) as well as 46, XY (6.67%, 3/45; χ 2 =146.25, P=0.000). All primary amenorrhea patients with deletion or break-point at Xp11.1-11.4 were short statures. Conclusions One of the main reasons of primary amenorrhea is choromosome abnormality, especially heterosome abnormality. It implies the need to routinely screen chromosomal anomalies for such patients. There might be relationship between Xp11.1-11.4 integrity and height improvement.