Fluorescence in situ hybridization (FISH) is a sensitive technique for molecular diagnosis of chromosomes on single cells and can be applied to sex determination of embryos. The objective has been to develop an accurate and reliable bovine Y chromosome-specific DNA probe in order to sex biopsed blastomeres derived from IVF bovine embryos by FISH. Bovine Y chromosome-specific PCR product derived from BtY2 sequences was labeled with biotin-16-dUTP (BtY2-L1 probe), and FISH was performed on karyoplasts of biopsed blastomeres and matched demi-embryos. Our FISH signal was clearly detected in nuclei of blastomeres of male embryos. FISH analysis of bovine embryos gave high reliability (96%) between biopsied blastomeres and matched demi-embryos. These results indicated that the BtY2-L1 bovine Y chromosome-specific FISH probe was an effective probe for bovine embryo sexing, and the FISH technique of probe detection could improve the efficiency and reliability.