RNA interference is a well established and widely used reverse genetic tool available for gene functional studies in trematodes. This technique requires the use of nonrelevant double-stranded RNA as control. However, several authors have reported inconsistencies associated with RNAi. We used RNASeq to analyze genes affected by nonspecific dsRNA exposure. We found only few genes presenting altered expression in schistosomula exposed to GFP or mCherry nonspecific-dsRNAs, most of them encoding uncharacterized proteins. Correlation analysis revealed that there are more differences among biological replicates, than due to treatment with nonspecific controls. These observations are of key relevance to other RNAi gene function assessment in other organisms.