Over the past 10 years, the widespread clinical applicability of semi-invasive and noninvasive diagnostic tools including medical thoracoscopy and ultrasonography has expanded the occurrence of pleural effusions to include several rare diseases such as granulomatous, connective tissue and autoimmune disorders including sarcoidosis, granulomatosis with polyangiitis (Wegener’s), systemic sclerosis, lupus erythematosus, rheumatoid arthritis, Sjögren’s syndrome, amyloidosis, Langerhans cell histiocytosis, and others. The purpose of this review is to summarize the current state of the knowledge regarding pathogenetic mechanisms of pleural involvement in rare disease entities and to highlight the need for more efforts to understand the underlying mechanisms for a more effective therapy.