Many genes involved in Drosophila melanogaster innate immune processes have been identified, but whether naturally occurring polymorphism in these genes leads to variation in immune competence among wild flies has not been tested. We report here substantial variability among wild-derived D. melanogaster in the ability to suppress infection by a Gram-negative entomopathogen, Serratia marcescens. Variability in immune competence was significantly associated with nucleotide polymorphism in 16 innate immunity genes, corresponding primarily to pathogen recognition and intracellular signaling loci, and substantial epistasis was detected between intracellular signaling and antimicrobial peptide genes. Variation in these genes, therefore, seems to drive variability in immunocompetence among wild Drosophila.