Nontuberculous mycobacteria (NTM) disease is a notifiable condition in Queensland, Australia. Mycobacterial isolates that require species identification are forwarded to the Queensland Mycobacterial Reference Laboratory, providing a central opportunity to capture statewide data on the epidemiology of NTM disease. We compared isolates obtained in 1999 and 2005 and used data from the Queensland notification scheme to report the clinical relevance of these isolates. The incidence of notified cases of clinically significant pulmonary disease rose from 2.2 (1999) to 3.2 (2005) per 100,000 population. The pattern of disease has changed from predominantly cavitary disease in middle-aged men who smoke to fibronodular disease in elderly women. Mycobacterium intracellulare is the main pathogen associated with the increase in isolates speciated in Queensland.