OBJECTIVE : Is there an association between the presence of sexually transmitted pathogens in the lower (LGT) and upper (UGT) female genital tract with endometriosis and infertility? METHODS : Case-control study with 60 women submitted to gynaecological laparoscopic surgery. Samples from the UGT and LGT were collected and analysed by single polymerase chain reaction (PCR) for human papillomavirus (HPV) and by multiplex PCR for other sexually transmitted infections (STI). Patients were initially divided into two clinical groups: infertile patients (n = 25) with conjugal infertility and fertile control patients (n = 35). After the surgical findings patients were further divided for additional analysis: an endometriosis group (n = 29) and non-endometriosis control group (n = 31). RESULTS : Sixty per cent of patients were positive for DNA-HPV in some of the genital tract sites sampled. Infertile patients were associated with high-risk HPV (hrHPV) positivity in the UGT sites (P = 0.027). The endometriosis group was associated with hrHPV positivity in the LGT and UGT sites (P = 0.0002 and P = 0.03, respectively). Only hrHPV types were detected in the UGT in both groups. It may be that there is a hrHPV infection continuum, from LGT to UGT, in infertile and endometriosis patients. No association was observed among the other seven STI studied. CONCLUSIONS : This study shows both an association between hrHPV infections in the UGT with infertility and endometriosis, and a possible hrHPV infection continuum, from LGT to UGT. Larger studies are needed to fully investigate the role of hrHPV as a cause of endometriosis and infertility.