Objective: To analyze the relationship between karyotypes and clinic features of patients with primary amenorrhea. Method: G-banding was employed in karyotype analysis of patients with primary amenorrhea. Results: Karyotype analysis of 468 patients with primary amenorrhea revealed that 255 patients (54.49%) had normal female karyotypes and 213 patients (45.41%) had abnormal karyotypes, including 143 patients with abnormal X chromosome, 4 patients with mosaic X-Y chromosome, 57 patients with 46,XY karyotype, 8 patients with abnormal autosome and one patient with X-autosome translocation. All primary amenorrhea patients with deletion or break-up in Xp11.1-11.4 were short in stature. Conclusion: One of the main reasons of primary amenorrhea was chromosome abnormalities, especially sex chromosome abnormalities. Karyotype analysis should be routinely applied to detect primary amenorrhea patients. Xp11-12 may be critical to development of stature.