AbstractA molecular understanding of synaptogenesis is a critical step toward the goal of understanding how brains “wire themselves up,” and then “rewire” during development and experience. Recent genomic and molecular advances have made it possible to study synaptogenesis on a genomic scale. Here, we describe the results of a screen for genes involved in formation and development of the glutamatergicDrosophilaneuromuscular junction (NMJ). We screened 2185P‐element transposon mutants representing insertions in ≈16% of the entireDrosophilagenome. We first identified recessive lethal mutants, based on the hypothesis that mutations causing severe disruptions in synaptogenesis are likely to be lethal. Two hundred twenty (10%) of all insertions were homozygous lethal. Two hundred five (93%) of these lethal mutants developed at least through late embryogenesis and formed neuromusculature. We examined embryonic/larval NMJs in 202 of these homozygous mutants using immunocytochemistry and confocal microscopy. We identified and classified 88 mutants with altered NMJ morphology. Insertion loci in these mutants encode several different types of proteins, including ATP‐ and GTPases, cytoskeletal regulators, cell adhesion molecules, kinases, phosphatases, RNA regulators, regulators of protein formation, transcription factors, and transporters. Thirteen percent of insertions are in genes that encode proteins of novel or unknown function. Complementation tests and RT‐PCR assays suggest that approximately 51% of the insertion lines carry background mutations. Our results reveal that synaptogenesis requires the coordinated action of many different types of proteins—perhaps as much as 44% of the entire genome—and that transposon mutageneses carry important caveats that must be respected when interpreting results generated using this method. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006