Urinary schistosomiasis is known to be associated with lesions in the female genital organs, particularly with the presence of ‘sandy patches’ in the lower genital tract. This study sought to determine the effect of treatment with praziquantel on gynaecological schistosomiasis in residents of an area endemic for Schistosoma haematobium. A cohort study was conducted among women aged 20–49 years in rural Zimbabwe. The shape and size of lesions were mapped pre treatment and 3 and 12 months following treatment. Ova of S. haematobium were looked for in cytology smears, wet mounts, biopsies, urine and stool. Specimens were collected for detection of sexually transmitted diseases and cancer. At baseline, almost half of the 527 women included in the study had sandy patches. Although urinary ova excretion decreased following treatment (odds ratio 10.3, 95% CI 3.8–27.8, P < 0.001), praziquantel treatment was not associated with a significant reduction in genital lesions or contact bleeding (P = 0.31–0.94). Sandy patches remained strongly associated with contact bleeding and vessel abnormalities even after treatment. Findings were independent of HIV status. Such lesions, which are common and apparently refractory to treatment for at least 12 months, may be an important risk factor for both the acquisition and transmission of HIV.