Human schistosome infections are chronic in nature and elevated IgG4 levels are associated with length of exposure. To examine how structure, localization and dynamics of exposure of a protein to the immune system can affect antibody isotype expression, specific antibody levels against two Schistosoma mansoni recombinant cathepsin molecules were determined in S. mansoni-infected individuals. Cathepsin B (rCatB, secreted in the gut) and cathepsin L (rCatL, localized in the reproductive structures) were used to determine IgG1 reactivity, as a measure of the stimulation of the immune response, and the switch to IgG4 as an indicator of the dynamics and rate of presentation to the immune system. Sera from three groups of S. mansoni-infected patients were used: individuals with life-long exposure in an endemic area in Burundi, a group from a recent endemic focus in Senegal, and of acutely infected European travellers. We report for the first time the ability of rCatL to trigger an immune response and show distinct antibody isotype reactivity between rCatB versus rCatL. Patients harbouring long-term chronic infections had elevated levels of IgG4 to both antigen, whereas individuals infected for less than four years had high IgG4 to rCatB but not to rCatL. Acutely infected travellers developed IgG1 to rCatB only. Our results demonstrate that an immune response is mounted more rapidly against a cathepsin molecule secreted in the gut of the worm than against an internally localized cathepsin.