Symbiotic nitrogen fixation by rhizobia in legume root nodules is a key source of nitrogen for sustainable agriculture. Genetic approaches have revealed important roles for only a few of the thousands of plant genes expressed during nodule development and symbiotic nitrogen fixation. Previously, we isolated >100 nodulation and nitrogen fixation mutants from a population of Tnt1-insertion mutants of Medigaco truncatula Using Tnt1 as a tag to identify genetic lesions in these mutants, we discovered that insertions in a M. truncatula nodule-specific polycystin-1, lipoxygenase, α-toxin (PLAT) domain-encoding gene, MtNPD1, resulted in development of ineffective nodules. Early stages of nodule development and colonization by the nitrogen-fixing bacterium Sinorhizobium meliloti appeared to be normal in the npd1 mutant. However, npd1 nodules ceased to grow after a few days, resulting in abnormally small, ineffective nodules. Rhizobia that colonized developing npd1 nodules did not differentiate completely into nitrogen-fixing bacteroids and quickly degraded. MtNPD1 expression was low in roots but increased significantly in developing nodules 4 d postinoculation, and expression accompanied invading rhizobia in the nodule infection zone and into the distal nitrogen fixation zone. A functional MtNPD1:GFP fusion protein localized in the space surrounding symbiosomes in infected cells. When ectopically expressed in tobacco (Nicotiana tabacum) leaves, MtNPD1 colocalized with vacuoles and the endoplasmic reticulum. MtNPD1 belongs to a cluster of five nodule-specific single PLAT domain-encoding genes, with apparent nonredundant functions.