Dermoscopy is an easily accessible, noninvasive diagnostic tool, originally used in the differentiation of benign and malignant skin tumors. Other structures beside pigment content observed by dermoscopy, e.g., scaling, follicles, or vessels, may present in aspecific pattern in different dermatoses. Recognition of these patterns may aid the diagnosis of inflammatory and infectious dermatological conditions. The aim of this article is to review the distinct dermoscopic features of granulomatous and autoimmune skin diseases. Diagnosis of granulomatous skin disorders is based on the histopathological examination. The dermoscopic picture of these diseases (cutaneous sarcoidosis, granuloma annulare, necrobiosis lipoidica, and granulomatous rosacea) show many similarities; however, there are some differences to note between the dermatoses, mainly in granuloma annulare. The cornerstones of the diagnostic process of autoimmune skin diseases (morphea, systemic sclerosis, dermatomyositis, cutaneous lupus erythematosus) include the clinical picture, immunoserology, and histology; however, dermoscopy may aid the diagnostic process and follow-up of the patients. For those diseases, where vascular abnormalities play an important role in the pathogenesis, videocapillaroscopy is used for examination of the microcirculation at the nailfold capillaries. Dermoscopy can be an easy-to-use everyday diagnostic tool in clinical practice regarding granulomatous and autoimmune skin diseases. Although punch biopsy is inevitable in many cases, the distinct dermoscopic structures can aid the diagnostic process.