Egg detection is the gold standard in diagnosing and controlling treatment in schistosomiasis, but sensitivity is poor in lightly infected individuals, whereas Schistosoma-specific antibodies are more sensitive. The purpose of the study was to evaluate use of Gut Associated Antigen (GAA) and Membrane Bound Antigen (MBA) assays in assessment of treatment efficacy and number of treated non-immune individuals with signs of treatment failure. In a retrospective study, residents in Denmark diagnosed with positive Schistosoma antibodies in the period 1987 - 2004 were offered follow-up including analyses for GAA, MBA, IgE and eosinophil count. Among 98 patients with positive antibody at time of diagnosis, 73 were examined for eggs and 27% had detectable eggs. 15% still had detectable living eggs after 1 course of treatment. At follow-up it was demonstrated that antibodies continued to increase for up to 6 months after treatment and average duration of positive GAA antibody was approximately 10 y. The study confirms that the GAA- and MBA-IFAT are not suitable in monitoring results of therapy. Treatment failure in 15% of non-immune patients indicates that studies are needed to define the correct dose of praziquantel in those individuals or to evaluate if resistance to praziquantel is a growing problem.