Objective To explore the molecular mechanisms of primary amenorrhea by using arrayCGH technology. Methods Ten patients with primary amenorrhea and 10 female volunteers with regular menstrual cycles as healthy controls were selected. All patients and control samples were analyzed by conventional chromosome analysis (G-banding technology) and array-CGH technology, respectively. ArrayCGH was performed using Affymetrix Cytogenetic 2. 7M arrays following the manufacturer's standard protocol. Results Both the patient group and control group analyzed by conventional G-banding karyotype technology showed a negative result with a normal female karyotype: 46, XX. The result of array-CGH analysis demonstrated a microdeletion of approximately 110 000 bp located at the end of the short arm of X chromosome [46, X, del (X) (p22. 33 )] were identified in 5 patients, which was not detected in the control group. All healthy control samples by array-CGH analysis showed no pathological DNA copy number variation. Conclusions Array-CGH technology can improve the diagnosis rate of chromosomal disease at the DNA level. It is necessary to provide array-CGH for higher resolution genetic analysis of idiopathic primary amenorrhea patient who can not be identified by conventional technology.