Background: Female genital schistosomiasis (FGS), caused by the parasite Schistosoma haematobium (Sh), is prevalent in Sub-Saharan Africa. FGS is associated with sexual dysfunction and reproductive morbidity, and increased prevalence of HIV and cervical precancerous lesions. Lack of approved guidelines for FGS screening and diagnosis hinder accurate disease burden estimation. This study evaluated FGS burden in two Sh-endemic areas in Southern Malawi by visual and molecular diagnostic methods. Methodology/Principal findings: Women aged 15–65, sexually active, not menstruating, or pregnant, were enrolled from the MORBID study. A midwife completed a questionnaire, obtained cervicovaginal swab and lavage, and assessed FGS-associated genital lesions using hand-held colposcopy. 'Visual-FGS' was defined as specific genital lesions. 'Molecular-FGS' was defined as Sh DNA detected by real-time PCR from swabs. Microscopy detected urinary Sh egg-patent infection. In total, 950 women completed the questionnaire (median age 27, [IQR] 20–38). Visual-and molecular-FGS prevalence were 26·9% (260/967) and 8·2% (78/942), respectively. 6·5% of women with available genital and urinary samples (38/584) had egg-patent Sh infection. There was a positive significant association between molecular- and visual-FGS (AOR = 2·9, 95%CI 1·7–5·0). 'Molecular-FGS' was associated with egg-patent Sh infection (AOR = 7·5, 95% CI 3·27–17·2). Some villages had high 'molecular-FGS' prevalence, despite <10% prevalence of urinary Sh among school-age children. Conclusions/Significance: Southern Malawi carries an under-recognized FGS burden. FGS was detectable in villages not eligible for schistosomiasis control strategies, potentially leaving girls and women untreated under current WHO guidelines. Validated field-deployable methods could be considered for new control strategies. Author summary: Female genital schistosomiasis (FGS) is a neglected gynaecological disease caused by the waterborne parasite Schistosoma (S.) haematobium. Despite over 45 million women are at risk of FGS in sub-Sahara Africa (SSA), approximately only 15,000 have been screened for the disease. Diagnosis is challenging and has traditionally required high technical expertise based on visual inspection for FGS typical lesions of the genital tract using a standard colposcope, seldom available in endemic settings. Closer-to the-user and decentralized strategies for FGS screening and diagnosis should be implemented to assess disease burden and scale-up FGS surveillance. This study was nested within the larger Morbidity Operational Research for Bilharziasis Implementation Decision (MORBID) cross-sectional project, aiming to correlate schistosomiasis-related morbidity data with village level endemicity across two districts in Southern Malawi. We found a significantly moderate to high burden of FGS (between 8–27% depending on diagnostic method used), with marked age differences in diagnostic performance. Further, some villages with low schistosomiasis prevalence (which would be excluded from control strategies per new WHO guidelines), had a significantly high burden of FGS, indicating the need for formal public health interventions. Within the remit of the sustainable development goals, this study's approach and findings emphasize the need of a field-deployable strategy to FGS screening and diagnosis in endemic areas in Malawi and other similar setting. [ABSTRACT FROM AUTHOR]