The only demonstrated mechanism for intracistronic genetic complementation requires physical interaction of protein subunits to create a functional molecule. We demonstrate another and perhaps quite general mechanism utilizing proteins with unique and shared domains. The Drosophila neural mutant Passover (Pas) disrupts specific synaptic connections. Alleles of a lethal complementation group exhibit a complex pattern of complementation with Pas alleles. Whereas all heterozygotes between these lethal alleles and Pas are viable, only some alleles complement the neural defect of Pas. Lethal and neural functions are separately encoded by two proteins that have distinct N-terminal domains and a common C-terminal portion. Neural-specific and lethal-specific mutations map to unique exons, while neural-lethal mutations map to shared exons. Combinations of lethal and neural alleles result in production of both proteins and demonstrate intracistronic complementation.