Preterm labour, premature prelabour rupture of membranes and low birth weight have all been associated with either specific maternal genital tract infections or an altered vaginal microflora during pregnancy. Factors that influence the variation in microbial–host interaction play an important role in individual susceptibility to adverse pregnancy outcomes. The innate immune responses at mucosal surfaces play a crucial role against microbial invasion. Multiple genes are responsible for the regulation of the innate immune system. Genetic polymorphisms that disrupt innate immune recognition or the responses to infectious microorganisms could explain the alterations in microflora and individual susceptibility to pregnancy complications.