We report for the first time in China, the characterization of a special abnormal inv(Y) with dual-color fluorescence in situ hybridization (D-FISH). We also study the mechanism of the formation of chromosome Y inversion and its relationship with the phenotype of recurrent spontaneous abortion. Using biotin-11-dUTP-labeled Yp11.3 breakpoint probe (No. 889) and CY3-labeled Yq12 heterochromatic region DNA probe (PY3.4), we performed D-FISH on a balanced translocation carrier with a [46,XY(90%)/46, X, inv(Y)(p11.3;q12)] karyotype determined by G-banding karyotyping, whose wife had recurrent miscarriages. The result of D-FISH shows that the percentage of cells with abnormal karyotypes is about 22%, higher than that determined by G-banding analysis. Moreover, besides the type of inversion diagnosed by G-banding, there are the two other abnormal karyotypes, including a type of chromatid inversion, which is difficult to be detected by conventional G-banding technique. The present of the three types of inversion confirms that the breakpoints of inv(Y) are heterogeneous. D-FISH is a powerful tool for the detection of chromosomal inversion due to its sensitivity and specificity.