Due to the rapid growth of the world’s population and the increasing demand for food, there is an urgent need for alternative, more sustainable sources of protein. Insects have an important role in the diet in some societies and current initiatives are exploring the potential that insects have to offer for the production of food and feed. In this context, the safety implications of both producing and consuming insects are an important aspect to investigate. Here we present a bioinformatics analysis of proteomics data obtained for larvae of four different species of fly to assess the homology of tropomyosin, arginine kinase and myosin light chain with the crustacean orthologous proteins and other known allergenic proteins. The results indicate that the three proteins share homology with known allergens and therefore it is likely that they are also potential allergens. The implications in relation to mass rearing of flies are discussed.