The detection of schistosomiasis cases among Belgian military personnel returning from a mission in the Democratic Republic of Congo (DRC) prompted a nested case-control study of all military personnel deployed in the DRC between 2005 and 2008 to identify all infections and to start appropriate treatment. Of 197 patients exposed at Lake Tanganyika in the Kalemie area of DRC, 49 (24.9%) were diagnosed with schistosomiasis. Swimming was significantly more frequent than wading in the seropositive group than in the seronegative group (88.9% vs. 73.6%; odds ratio [OR], 2.86; 95% confidence interval [CI], 0.97-9.01). Thirty-one of 49 patients (63.3%) were symptomatic; including skin problems in 34.7%, respiratory symptoms in 12.2%, fever in 14.3%, and 51.0% with gastrointestinal problems. Median eosinophil counts were significantly higher in seropositive patients (375 vs. 138 per tL; Wilcoxon rank sum test [Ws] = 10,559.00; p < 0.01; r = -0.49). In total, 20 (40.8%) of the 49 patients were treated for symptomatic infections and the remainder for asymptomatic schistosomiasis. Our study emphasizes the need for active systematic post-tropical screening in military personnel after deployment to Schistosoma-endemic regions of the world.