Genetically modified (GM) plants might affect ecosystem functioning through effects on non-target decomposer organisms, which play an important role in the decomposition of organic matter and nutrient release. These organisms can be affected directly by the transgene products, or indirectly by pleiotropic effects, which may influence the composition of plant compounds, such as the lignin content or the C/N ratio that could even modify matter flux. Therefore, an ecological risk assessment for GM plants also has to include decomposers. In a laboratory diet experiment, we investigated possible effects of transgenic antifungal wheat on two saprophagous Diptera species, the drosophilid Drosophila melanogaster and the phorid Megaselia scalaris. We used several experimental transgenic wheat varieties with a specific antifungal powdery mildew resistance (Pm3b) and varieties with a broad antifungal resistance, which is based on the expression of chitinase and glucanase. We determined if important fitness parameters, such as fertility, development time and sex ratio differed when the two saprophagous Diptera species were fed with either leaves of transgenic or non-transgenic wheat. To include potential long-term effects, we performed our experiments over four fly generations. Additionally, we analysed the C/N ratio, and the cellulose, hemicellulose and lignin contents of the different wheat lines to investigate any changes in the diet composition, which may alter food quality through potential pleiotropic effects. We found occasional differences in development time or the number of offspring for both dipteran species in several investigated diet comparisons but we found no consistent pattern of GM wheat effects on the tested dipteran species. Though some wheat lines showed an altered chemical composition, possibly indicating a pleiotropic effect, we found no correlation between diet quality of the wheat lines and fitness parameters. Our study shows also that dipterans represent useful model species with M. scalaris being the most suitable species, and that our experimental approach is an appropriate laboratory method to investigate the decomposition of GM material by insect larvae.