While rare mutations in the GM-CSF receptor α or β chains (CSF2RA, CSF2RB)8, the surfactant proteins B or C9, ATP-binding cassette subfamily A member 3 (ABCA3)10, and thyroid transcription factor-111 were identified as causing hereditary PAP, the genetic basis underlying autoimmune PAP (aPAP) has never been thoroughly investigated due to its low prevalence. Here, ABCA3 is linked to autoimmune pulmonary alveolar proteinosis.