Schistosoma real-time polymerase chain reaction (PCR) is sensitive and specific in urine and stool. We sought to explore the relationship between genital schistosomiasis and the Schistosoma PCR in women. PCR was run on 83 vaginal lavage samples from a rural Zimbabwean population. Women underwent clinical and colposcopic investigations, analyses for sexually transmitted infections, and genital schistosomiasis. Thirty samples were positive for Schistosoma PCR: 12 were strong and 18 were weak positive. Sensitivity (67%) and specificity (83%) were best in women below the age of 25 years. A positive schistosome PCR result was associated with S. haematobium ova in genital tissue, so-called sandy patches, and bleeding. Prevalence determined by PCR were lower and real-time PCR values were weaker in older women. The presence of Schistosoma DNA may be greater in the recent lesions (e.g., in younger women). For diagnosis in rural areas and in large studies, Schistosoma PCR could become a supplement to gynecologic examinations.