The influence of contraception on vaginal microflora can have a major impact on the risk of developing acute or recurrent vaginal infections, but also may influence the risk of acquiring sexually transmissible infections (STI) such as HIV. A cohort of 248 women presenting for levonorgestrel-releasing intrauterine system (LNG-IUS) insertion or reinsertion were stratified according to their current contraceptive method. Information concerning their menstrual pattern and data about the medical history were collected. The composition of their vaginal microflora was studied by detailed phase contrast microscopy of fresh vaginal fluid, and aerobic cultures were taken to detect enteric bacterial growth and fungal colonisation. LNG-IUS and progesterone-only-pill (POP) users had significantly lower blood loss (p < 0.001) than other women. Regardless of the type of contraception used, all women reported similar rates of symptomatic lower genital tract infection during the preceding year. Women using combined oral contraception (COC) and long-term LNG-IUS had the same bacterial composition of vaginal microflora as non-contraceptive users, even when infections were combined. Both hormonal and non-hormonal intrauterine device users had an increased tendency to have more vaginal colonisation with Candida. Women on POPs or subcutaneous implants had a tendency towards increased vaginal atrophy, but had a lower Candida carriage rate compared to IUCD users (LNG-IUS and Copper-IUCD, p = 0.037). Women with an increased risk of acquiring STIs or recurrent BV could benefit from LNG-IUS or COC due to a well-preserved vaginal bacterial flora. Women with a susceptibility for RVVC should prefer POPs, and avoid intrauterine contraception.