Summary We report a Japanese patient with Hermansky–Pudlak syndrome (HPS) who developed systemic lupus erythematosus (SLE). This is the second case report of HPS complicated with SLE. A 1-bp duplication of adenine at codon 441 was found in the HPS gene, namely HPS1, which caused a frameshift. This case serves as evidence indicating that a patient with HPS can be predisposed to SLE.