While both cause sinus tracts and abscesses in intertriginous areas, cutaneous Crohn's is distinguished by the presence of characteristic "knife-cut" fissures and its direct association with underlying gastrointestinal Crohn's disease.
A pilonidal sinus is specifically located in the midline of the natal cleft, a distinct location from the genital or perianal lesions of cutaneous Crohn's disease.