Sex determination of bovine embryos in conjunction with embryo transfer is an established method to maximize efficiency by producing offspring with the preferred gender. Present methodology for sexing embryos is based on PCR, which requires molecular laboratory equipment, trained personnel, and several hours before a result becomes known. We developed a simple, rapid, non-PCR procedure for identification of Y-chromosomes in bovine blastomeres recovered via biopsy. A biopsy (n = 5 to 8 blastomeres) was taken from a blastocyst-stage embryo and transferred onto a plastic slide. After drying and fixation, the cells were denatured and incubated with a peptide nucleic acid probe designed to target unique Y-chromosome specific sequence. The probe was conjugated to a fluorescent dye (CY-3) which enables Y-chromosome detection as a bright spot within blastomere nuclei when using a fluorescent microscope. The absence of signal indicates female embryonic DNA. From placement of the biopsy onto a plastic slide, the methodology required approximately 75 minutes to determine embryo gender. The accuracy of the biopsy sexing procedure was demonstrated by parallel gender determination of the same embryo using an established PCR method designed for the bovine amelogenin locus. Based on 18 in vitro-produced bovine embryos generating a result for both assays, there was a 94.4% match (17/18) of gender assignment. The present technology represents a simple alternative to PCR-based embryo sexing technology. Research is ongoing for future development of live embryo sexing determination.