In the present study, we examined the effect of two-step and sequential culture systems on the development, quality, and gene expression profile of bovine embryos generated by in vitro fertilization. Presumptive zygotes were randomly allocated to four culture treatments: (1) KSOM + 0.4% BSA for 3 days, and then KSOM + 5% FBS to day 7 (K-K/FBS); (2) KSOM + 0.1% BSA for 3 days, and then SOF + 5% FBS to day 7 (K-S/FBS); (3) KSOM + 0.1% BSA for 3 days, and then SOF + 0.8% BSA to day 7 (K-S/BSA); and (4) KSOM + 0.4% BSA for 3 days, and then KSOM + 0.8% BSA to day 7 (K-K/BSA). Culture medium had no effect on cleavage rate. However, a significant difference (P < 0.01) was observed with the two-step culture systems, yielding higher rate of blastocysts (37 and 32% for K-K/FBS and K-K/BSA, respectively) compared to sequential culture systems (26 and 28% for K-S/FBS and K-S/BSA, respectively). Embryos cultured in sequential K-S/FBS developed slowly, had a lower hatching rate, fewer cells, and a higher apoptosis rate compared to other treatments. Gene expression analysis showed alterations of DNMT1, OCT-4, and SOD2 in embryos cultured in sequential K-S/FBS and SOD1 in embryos cultured in two-step K-K/BSA. In conclusion, in vitro culture systems may have an impact not just in the developmental potential and quality of the generated embryos but also in the gene expression profile, which suggests that changes in the culture medium composition can modulate global gene expression.