Methotrexate (MTX), a synthetic folate analog, is a tight-binding inhibitor of dihydrofolate reductase (DHFR), a key enzyme for the biosynthesis of purines, thymidylate, and several amino acids. As a consequence, MTX decreases titres of reduced folates, interferes with DNA synthesis, and results in the arrest of rapidly proliferating cells, making it a drug of choice for the treatment of a variety of cancers and auto-immune disorders. MTX is also a known teratogen in all higher animals tested, but there is little information about the effects of this drug on invertebrates. Here we show that MTX has little effect on the survival of Drosophila melanogaster adult flies, but severely diminishes female fecundity. Reduced oviposition, coupled with aberrant egg morphologies, resulted in near sterility of MTX-treated females. Rare surviving progeny showed developmental abnormalities including larval tumors, and bristle, wing, eye, and leg defects. To determine if these phenotypes could be attributed solely to DHFR inhibition, microarray analysis was undertaken and included MTX-treated females, ovaries, and cell line samples. Genes encoding transcripts that were perturbed by the drug were verified using quantitative real-time RT-PCR. Many of these genes were involved in cell cycle regulation, signal transduction, transport, defense response, transcription, or various aspects of metabolism. These studies show that MTX treatment has multiple targets and, in addition, provides a new invertebrate model for the study of teratogenesis.