The purpose of this study was to compare the endocervical microflora of women in preterm and term labour and to determine whether the presence of a specific microflora is significantly associated with preterm labour. A prospective study was performed in Lithuania among 212 women in preterm labour (latent phase, n = 110; active phase, n = 102) and among 62 healthy women in term labour. Microbiological assessment included cultures for aerobic bacteria, yeasts, and Trichomonas vaginalis and direct immunofluorescence reaction for Chlamydia trachomatis, Escherichia coli (odds ratio 8.16; 95% confidence interval 1.27–340.23) and Staphylococcus aureus (odds ratio 7.79; 95% confidence interval 1.21-325.40) were significantly more often isolated from women in preterm than from women in term labour. The prevalence of C. trachomatis was the same in the preterm and in the term labour group. The pregnancy outcome during the latent or the active phase of preterm labour with or without C. trachomatis infection did not differ. It is concluded that E. coli and S. aureus are significantly more prevalent in endocervical cultures from Lithuanian women in preterm than from those in term labour.