The pregnancy rate is lower in mares inseminated at the first post-partum (p.p.) oestrus (40-50%) compared with pregnancy rates in subsequent oestrous cycles (55-65%). The causes of the lowered pregnancy rate are not fully understood. The aim of the present study was to examine if embryonic defects could be one of the reasons for lowered pregnancy rate. A total of 23 p.p. and 14 non-lactating control mares were flushed 7 days after detection of ovulation. Embryo recovery rate was 48% and 71% in p.p. and control mares, respectively (p = 0.16). Embryos were photographed, measured, graded and stained with fluorescein diacetate to assess their viability. Thereafter embryos were bisected and stained with Hoechst 33342 to count the cell nuclei. Embryos in both groups were equally viable and the cell numbers were not significantly different. According to morphological evaluation all embryos were classified as excellent or good. Embryos aged 7.3 to 7.6 days (+/-0.25 days) were smaller in the p.p. group than in the control group (p < 0.05). Forty-seven (9/19) and 8% (1/13) of the uterine swabs, taken before the first insemination, yielded bacteria and neutrophils in p.p. and control mares, respectively. The amount of neutrophils and/or bacteria had no statistically significant effect on embryo recovery rate (p > 0.10). Recovery of embryos was not related to histological findings in uterine biopsies taken after embryo recovery. Embryo recovery rate in p.p. mares (48%) was similar to previously reported foal heat pregnancy rates (40-50%). Hence, early embryonic death in utero would not be the most likely reason for lowered pregnancy rate in mares inseminated at the first p.p. oestrus. Sperm transport and oviductal conditions by the time of the first p.p. oestrus would need to be studied to clarify the role of fertilisation failure as the cause of lower pregnancy rate in mares inseminated at foal heat.