The study was designed to determine the prevalence of genital mycoplasmas, ureaplasmas and Chlamydia on women attending their first prenatal visit, in conjunction with pre-term labour or HIV status. For pre-term labour (2003), 199 women were monitored for pre-term delivery (<37 weeks); for colonisation and HIV (2005), 219 women were screened. Microbial detection was performed on DNA extracted from endocervical swabs employing PCR techniques. Colonisation was seen to be highest in the 14-20 year age group from 2003. In women aged > or = 21 years, co-colonisation was 13%, although there was a shift from co-colonisation with Mycoplasma hominis and Ureaplasma urealyticum in 2003, to other dual/triple combinations in 2005. Overall, major trends from both collection periods were that the prevalence of U. urealyticum tended to be higher in women > or = 26 years, while the prevalence of Chlamydia trachomatis and M. hominis lower. No association was evident between colonisation with M. hominis, U. urealyticum, Ureaplasma parvum and labour outcome. HIV status had no effect on the prevalence/co-colonisation of M. hominis, U. urealyticum or C. trachomatis. The importance of genital mycoplasmas, ureaplasmas and C. trachomatis in long-term aetiologies requires further investigations, certainly in relation to syndromic management regimens that fail to reduce colonisation rates.