Background: Schistosomiasis is a disease of world-wide importance and is caused by parasitic flatworms of the genus Schistosoma. These parasites exhibit a unique reproduction biology as the female s sexual maturation depends on a constant pairing-contact to the male. Pairing leads to gonad differentiation in the female, and even gene expression of ... some gonad-associated genes is controlled by pairing. In contrast, no morphological changes have been observed in males, although first data indicated an effect of pairing also on gene transcription in males. Methodology/Principal Findings: To investigate the influence of pairing on males, we performed a combinatory approach applying SuperSAGE and microarray hybridization, generating the most comprehensive data-set on differential transcription available to date. Of 6,326 sense transcripts detected by both analyses, 29 were significantly differentially transcribed. Besides mutual confirmation, the two methods complemented each other as shown by data comparison and real-time PCR, which revealed a number of genes with consistent regulation across all methods. One of the candidate genes, follistatin of S. mansoni (SmFst) was characterized in more detail by in situ hybridization and yeast two-hybrid (Y2H) interaction analyses with potential binding partners.Conclusions/Significance: Beyond confirming previously hypothesized differences in metabolic processes between pairingexperienced (EM) and pairing-unexperienced males (UM), our data indicate that neuronal processes are involved in malefemale interaction but also TGFb-signaling. One candidate revealing significant down-regulation in EM was the TGFbpathway controlling molecule follistatin (SmFst). First functional analyses demonstrated SmFst interaction with the S. mansoni TGFb-receptor agonists inhibin/activin (SmInAct) and bone morphogenic protein (SmBMP), and all molecules colocalized in the testes. This indicates a yet unknown role of the TGFb-pathway for schistosome biology leading to male competence and a possible influence of pairing on the male gonad.