Pulmonary alveolar microlithiasis is an autosomal recessive disorder in which microliths are formed in the alveolar space.To identify the responsible gene that causes pulmonary alveolar microlithiasis.By means of a genomewide single-nucleotide polymorphism analysis using DNA from three patients, we have narrowed the region in which the candidate gene is located. From this region, we have identified a gene that has mutations in all patients with pulmonary alveolar microlithiasis.We identified a candidate gene, SLC34A2, that encodes a type IIb sodium phosphate cotransporter and that is mutated in six of six patients investigated. SLC34A2 is specifically expressed in type II alveolar cells, and the mutations abolished the normal gene function.Mutations in the SLC34A2 gene that abolish normal gene function cause pulmonary alveolar microlithiasis.