We present a case of a patient with cystic fibrosis who was thought to be colonized with Mycobacterium abscessus for 13 yr prior to developing clinically apparent mycobacterial infection. However, histologic evidence indicated that invasive mycobacterial disease was present from the onset. While accepting that chronic endobronchial colonization with atypical mycobacteria may occur in patients with cystic fibrosis, the repeated isolation of mycobacteria from the sputum of these patients should alert the clinician to the possibility of indolent disease. Early consideration of treatment for this infection should occur in any patient with cystic fibrosis in whom there is an unexplained deterioration in lung function. The recent introduction of high dose ibuprofen raises concerns about its possible contribution to the progression of the infection.