The 64-year-old female patient with cough and intermittent hemoptysis of six months duration visited our hospital. On chest computed tomography, a small, ovoid, 1.3cm sized and well enhanced lesion was detected on the distal trachea. Two multiple lobulated lesions on the sigmoid and transverse colon were revealed on the colonoscopy. The histological findings showed small and medium sized lymphocytes infiltration, CD20 and CD79a positive staining and multiple lymphoepithelial lesions on the distal trachea and colon tissues. Herein, a case of primary MALT lymphoma, with involvement of the trachea and colon, which was treated with rituximab (CD20 anti-monoclonal antibody), cyclophosphamide, adriamycin, vincristine and prednisolone (CHOP regimen), is reported.