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An increasing incidence in disease caused by nontuberculous mycobacteria is being reported. We investigated the burden of disease in immunocompetent German children in a prospective nationwide study from April 2003 to September 2005. Ninety-seven percent of children presented with lymphadenitis; median age was 2.5 years. Using the capture-recapture method, we estimated a cumulative incidence rate of 3.1/100000 children.