Microscopic polyangiitis is a type of antineutrophil cytoplasmic antibody-associated vasculitis, characterized by a systemic, pauci-immune, necrotizing, small-vessel vasculitis without clinical or pathological evidence of necrotizing granulomatous inflammation. Many studies have linked autophagy-related gene polymorphisms to the development of immune diseases. However, the association between autophagy-related genes and microscopic polyangiitis remains unclear.We investigated the association between microscopic polyangiitis and the single nucleotide polymorphism rs807185 in autophagy-associated gene 4A (ATG4A) in the Chinese population.ATG4A single nucleotide polymorphism rs807185 frequency was identified using multiplex polymerase chain reaction and high-throughput sequencing in a cohort with microscopic polyangiitis (n = 181) and a healthy control group (n = 209).We found that the control cohort had a higher prevalence of allele A of rs807185 compared to the microscopic polyangiitis cohort. The rs807185A allele was therefore linked to a lower risk of microscopic polyangiitis.The single nucleotide polymorphism rs807185 allele A in ATG4A may have a protective effect against microscopic polyangiitis in the Chinese population, but the molecular mechanisms remain unclear.