In order to optimize the production of embryos under tropical conditions and to test a possible seasonal effect on embryo quality, 40 Zebu cows were superovulated during the dry season (April to May) and during the rainy season (July to August). A total of 116 (average 2.7/cow) and 83 embryos (3.5 average/cow) were obtained during the respective seasons. After classification as good, fair or poor quality, embryos were tested based on their ultrastructural differences (n = 53 dry season 16 good, 20 fair and 17 poor and n = 61 rainy season 21 good, 20 fair and 20 poor) and their degree of apoptosis using the TUNEL technique (n = 30 during the dry season and n = 55 in the rainy season). Structural characteristics determining embryo quality varied between good and fair quality embryos. No difference, however, was observed between good, fair and poor quality embryos from the two seasons. The number of TUNEL-positive cells was different among embryos (p < 0.001), being lower in labelled cells of good quality embryos regardless of the season. Fewer apoptotic cells were observed in embryos assigned in all three quality levels during the rainy season (p < 0.001). Ultrastructural evaluations confirmed the results obtained by TUNEL. Cryopreserved embryos of good (n = 25 in each season) and fair quality (n = 11 dry season; n = 17 rainy season) showed a significant decrease of TUNEL-positive cells during the rainy season (p < 0.05). Results suggest that embryos collected in the dry season have more cellular damage in contrast; embryos cryopreserved in the rainy season appeared morphologically better equipped to result in a pregnancy following transfer.