In cases showing organizing pneumonia (OP) with radiologic findings and pathological images, it is necessary to differentiate between idiopathic and secondary diseases as the cause of OP. Cryptococcus infection as a cause of OP is not well known. We herein report two cases of secondary pulmonary cryptococcosis in immunocompromised patients who showed OP, and the usefulness of bronchoscopy and serum cryptococcal antigen test for an early diagnosis. Common to both cases was that antibiotic therapy and corticosteroid therapy were ineffective, while antifungal agents were effective. In cases of immunocompromised patients who present OP with radiologic findings or pathological images, prompt administration of antifungal treatment at an early stage is important when pulmonary cryptococcosis is identified by bronchoscopy and serum cryptococcal antigen test.