Backgrounds and objectives <p>Autoimmune pulmonary alveolar proteinosis (aPAP) is a rare lung disorder, and its long-term clinical outcomes, underlying determinants, and temporal dynamics of serum autoantibody levels remain poorly characterized.</p> Methods <p>This single-center retrospective observational study comprised 64 patients diagnosed with aPAP, all of whom had been monitored for a minimum of three years following disease onset. Clinical courses were evaluated using disease severity score (DSS), based on arterial oxygen tension and respiratory symptoms. Serum anti–granulocyte-macrophage colony-stimulating factor (GM-CSF) IgG autoantibody (αGM) levels were quantified by enzyme-linked immunosorbent assay.</p> Results <p>Among 64 patients with any DSS, 45.3% showed clinical improvement, 40.6% remained stable, and 14.1% experienced deterioration over median follow-up period of 7.8 years. In a binary logistic regression analysis excluding patients with an initial DSS of 1, for whom improvement was not feasible, higher initial DSS, higher baseline % forced vital capacity, and the absence of fibrotic patterns on computed tomography were identified as significant explanatory variables associated with DSS improvement, whereas whole lung lavage (WLL) and GM-CSF inhalation were not in the comparison of the initial and final DSS. Longitudinal assessment of serum αGM levels in 52 patients revealed a decline in 98% of them (<i>n</i> = 51) with an estimated antibody half-life of 3.5 years. GM-CSF inhalation therapy was significantly associated with lower final antibody levels adjusted for initial level and the interval between the initial and final measurements by analysis of covariance.</p> Conclusions <p>The overall decline in αGM levels observed in this study may suggest a favorable or stable long-term prognosis in aPAP; however, further longitudinal investigations are warranted to confirm this presumed association.</p>