The autoimmune manifestations of primary immunodeficiencies, such as autoimmune lymphoproliferative syndrome (ALPS) and common variable immunodeficiency (CVID), often constitute a great therapeutic challenge and have a significant impact on patients' morbidity and mortality. The most common autoimmune presentations are autoimmune cytopenias, but organ-related autoimmunity is also frequently observed. From a pulmonology perspective, granulomatous/lymphocytic interstitial lung disease (GLILD) is a severe immunological complication which significantly worsens the clinical outcome of these patients and for which there are currently few guidelines or protocols for treatment. We present three cases where the use of Mycophenolate in the context of autoimmune cytopenias proved beneficial also on the lung disease.