The aim of this study was to carry out a cytological and microbiological comparative investigation of vaginal microflora in pregnant ewes. The subjects for the study comprised of 39 healthy curly fleeced breed ewes (n= 39), approximately 3 years old, at 2-4 months of pregnancy. Two vaginal samples were taken for cytological and microbiological examinations from each ewe in a sterile manner. Hemacolor (R) was used in cytological examination, while microbiological analysis were completed by conventional techniques. In cytological examination, slides were evaluated to detect lactobacilli, other bacteria, "clue cell" formation and presence of neutrophils. Microbiological investigation was carried out to detect possible pathogens. Cytological results compatible with bacterial vaginosis were obtained in 10 cases. Microbiologically, single type bacteria in 27 cases and more than one bacterium in 12 cases were isolated. The most common isolated pathogen was Escherichia coli. Comparing the cytological and microbiological results, 7 out of 27 cases were compatible with the bacterial vaginosis. In 3 cases of bacterial vaginosis non-pathogenic agents were revealed. In conclusion, it was proven that utilising the cytological examination provides more reliable results for detection of normal vaginal microflora of pregnant ewes.