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Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder characterized by oculocutaneous albinism and a lack of dense granules in platelets. HPS types 1 and 4 are associated with a granulomatous enterocolitis that is phenotypically indistinguishable from Crohn’s disease. We present two cases of HPS-associated Crohn’s disease phenotype in which the patients were refractory to standard medical management. The pathophysiology of HPS is mediated by single-gene defects that alter endosome trafficking, and we hypothesize that this mechanism leads to the observed association with a CD phenotype.