In October 1998, cohorts of circular migrant men and their non-migrant sexual partners, and non-migrant men and their non-migrant sexual partners from rural South Africa were recruited and followed-up every 4 months until October 2001. At each visit, information on sociodemographic, sexual behaviour, sexually transmitted infections (STIs) and HIV was collected. In total, 553 individuals aged between 18 and 69 years were recruited. A man and his sexual partner(s) form a sexual partnership. Migration status, age, marital status, age at sexual debut, recent sexual partners and HIV status were found to be important determinants of STI. The risk of STI varies (sigma2 = 1.45, P < 0.001) significantly across sexual partnerships even after controlling for important determinants. The variance implies substantial correlation (0.59) between members of the same sexual partnership. Ignoring this correlation leads to incorrect inference. Migration contributes significantly to the spread of STIs. Community interventions of HIV/STI should target co-transmitter sexual partnerships rather than high-risk individuals.