We examined 1,022 free-living roe deer, red deer, and fallow deer for mycobacteria in Germany, 2002-2006. Retropharyngeal lymph nodes and other tissues were processed for culture and isolates were identified with the use of polymerase chain reaction and DNA sequencing. Mycobacteria were found in 18.3% of deer, with Mycobacterium avium in 14.8%. Other atypical mycobacteria were detected in 5.3%. Members of the Mycobacterium tuberculosis complex were not detected.