Epigenetic differences between male and female bovine blastocysts provide a plausible link between physiological and gene transcription differences observed between male and female embryos. The aim of this study was to examine gender-related epigenetic differences in bovine blastocysts produced in vitro. Oocytes were matured in vitro and inseminated with frozen-thawed sex-sorted (X or Y) and unsorted (control) bull sperm. Zygotes were cultured to blastocyst stage and were analyzed for embryo sexing, mtDNA content, telomere lengths, methylation analysis, and quantification of mRNA transcripts of DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) HMT1 hnRNP methyltransferase-like 2 (Hmt1), and interleukin enhancer binding factor 3 (Ilf3). There was a difference (P<0.05) in the mean mtDNA copy number between male (410,000±23,000) and female (360,000±21,000) blastocysts. Telomere length was shorter in male blastocysts (p<0.01). The level of methylation in a sequence near a variable number of tandem repeats minisatellite region (VNTR) in males (39.8% ± 4.8) was higher than in females (23.7% ± 3.1) (P<0.05); however, no differences were found in other regions analyzed. Moreover, transcription differences between genders were observed for Dnmt3a, Dnmt3b, Hmt1, and Ilf3. These results provide evidence of epigenetic differences between male and female bovine in vitro produced embryos and suggest that before initiation of gonadal differentiation, epigenetic events may modulate the difference between speed of development, metabolism and transcription observed during preimplantation development between male and female embryos.