We included 92 pairs of ewes with or without retention of fetal membranes in a cohort study of 25 flocks in Southern Greece. We obtained two uterine content samples under aseptic conditions, by introducing a swab into the uterus of these ewes, on the 2nd-4th and the 5th-9th day after lambing. We used conventional bacteriological techniques to isolate and identify bacteria and to carry out antimicrobial agents susceptibility testing. The prevalence of bacterial intrauterine contamination among ewes with retention was 24% on the first and 46% on the second sampling (P < 0.0001) and that among ewes without retention was 8 and 2% (P > 0.05), respectively. Clinical signs accompanying the retention of fetal membranes were more frequently observed among ewes with intrauterine contamination than among those without (P = 0.0007). The odds of an ewe having an intrauterine contamination increased multiplicatively by 1.06 when the median duration of retention in the flock increased by 6 h. The principal bacteria isolated from the ewes with retention were Arcanobacterium pyogenes and Escherichia coli; 21% of 73 isolates tested were found resistant to at least one antimicrobial agent.