RATIONALE: Few population-based data are available regarding nontuberculous mycobacteria (NTM) pulmonary disease epidemiology and prognosis. OBJECTIVES: To examine NTM pulmonary colonization incidence, disease incidence, and prognostic factors. METHODS: All adults in Denmark with at least one NTM-positive pulmonary specimen during 1997-2008 were identified using national medical databases and were categorized as having possible or definite NTM disease or colonization. MEASUREMENTS AND MAIN RESULTS: We calculated annual age-standardized NTM incidence rates and adjusted hazard ratios (HR) of death associated with patient age, sex, comorbidity, NTM species, and NTM disease status. Of 1,282 adults with 2,666 NTM-positive pulmonary specimens, 335 (26%) had definite NTM disease, 238 (19%) possible disease, and 709 (55%) colonization only. NTM incidence rates decreased until 2002, followed by an increase from 2003 to 2008 (mean annual rate per 100,000 person-years: NTM colonization, 1.36; NTM disease, 1.08). Five-year mortality following definite NTM disease was 40.1%. After controlling for potential confounders, 5-year mortality for definite NTM disease was slightly higher than for NTM colonization (adjusted HR: 1.15, 95% CI 0.90-1.51). M. xenopi was associated with worse prognosis (adjusted HR: 1.51, 95% CI 0.99-2.33) than the reference Mycobacterium avium complex. High comorbidity level (HR 2.97), age >/= 65 years (HR 9.17), and male sex (female sex HR 0.73) were predictors of death. CONCLUSIONS: NTM disease incidence has remained unchanged in Denmark over the past 12 years. Patients with NTM colonization and disease have similarly poor prognosis. Negative prognostic factors include high levels of comorbidity, advanced age, male sex, and M. xenopi.