OBJECTIVE To evaluate the diagnostic value of fluorescence in-situ hybridization (FISH) in sex chromosome abnormality. METHODS alpha-satellits DNA probes of X, Y chromosomes were used to FISH with blood samples from 19 patients with primary anemia or of gonad dysplasia. Five infertile men who were detected abnormal by G-banding analysis during metaphase and interphase. Samples from healthy men and women were used as positive controls and reactions with hybridization fluid without probes as negative controls. RESULTS The karyotypes, 45, X; 45, X/46, XX/47, XXX; 45, X/46, XY; 47, XXY; 45, X/46, XXX were detected by FISH. Others were not detected by G banding such as 45, X/46, X,r? 46, X,r? but were found to be 45, X/46, X,r(X), 46, X, r(X), by FISH technique, confirming to be X ring chromosome. A female patient whose karyotype was 45, X/46, X, mar. by G banding. But G banding technique could not analyze the property of the marker and FISH revealed the marker was dici(yq), that is dicentric chromosome Y with two long arms of equal length. The real karyotype was 45, X/46, X, dici(yq) mosaicism. It belonged to Y chromosome abnormal and gonadal dysplasia syndrome. CONCLUSIONS FISH can help to detect those chromosome abnormalities which can not be confirmed by traditional cytogenetics. It is of value in studying the complex chromosome mutation such as sex chromosome abnormality, unknown little marker, ring chromosome, mosaiciasm and translocation.