Schistosomiasis is a neglected disease with large geographic distribution worldwide. Among the several different species of this parasite, S. mansoni is the most common and relevant one; its pathogenesis is also known to vary according to the worms' strain. High parasitical virulence is directly related to granulomatous reactions in the host's liver, and might be influenced by one or more molecules involved in a specific metabolic pathway. Therefore, better understanding the metabolic profile of these organisms is necessary, especially for an increased potential of unraveling strain virulence mechanisms and resistance to existing treatments. In this report, MALDI‐MSI and the metabolomic platform were employed to characterize and differentiate two Brazilian S. mansoni strains: males and females from Belo Horizonte (BH) and from Sergipe (SE). By performing direct analysis, it is possible to distinguish the sex of adult worms, as well as identify the spatial distribution of chemical markers. Phospholipids, diacylglycerols and triacylglycerols were located in specific structures of the worms' bodies, such as tegument, suckers, reproductive and digestive systems. Lipid profiles were found to be different both between strains and males or females, giving specific metabolic fingerprints for each group. This indicates that biochemical characterization of adult S. mansoni may help narrowing‐down the investigation of new therapeutic targets according to worm composition, molecule distribution and, therefore, aggressiveness of disease. Copyright © 2014 John Wiley & Sons, Ltd.