Schistosoma haematobium causes female genital schistosomiasis (FGS), which is a poverty-related disease in sub-Saharan Africa. Furthermore, it is co-endemic with human immunodeficiency virus (HIV), and biopsies from genital lesions may expose the individual to increased risk of HIV infection. However, microscopy of urine and hematuria are nonspecific and insensitive predictors of FGS and gynecological investigation requires extensive training. Safe and affordable diagnostic methods are needed. We explore a novel method of diagnosing FGS using computer color analysis of colposcopic images. In a cross-sectional study on young women in an endemic area, we found strong associations between the output from the computer color analysis and both clinical diagnosis (odds ratio [OR] = 5.97, P < 0.001) and urine microscopy for schistosomiasis (OR = 3.52, P = 0.004). Finally, using latent class statistics, we estimate that the computer color analysis yields a sensitivity of 80.5% and a specificity of 66.2% for the diagnosis of FGS.