The objective of the current study was to identify factors associated with avian mycobacteriosis in zoo birds. Inventory data, population health records, and necropsy data from eligible birds in the Zoological Society of San Diego's (ZSSD) collection from 1991-2005 (n = 13,976) were used to describe disease incidence, prevalence, and postmortem findings. A matched case-control study was then conducted to identify factors describing demographic, temporal, and enclosure characteristics, along with move and exposure histories. Cases (disease-positive birds; n = 167) were matched in a 17 ratio with controls (disease-negative birds; n = 1169) of similar age and taxonomic grouping. Potential risk factors were evaluated using univariate and multivariable conditional logistic regression. Disease prevalence and incidence were estimated for the study period at 1.2% and 3 cases/(1,000 bird-years at risk), respectively. Lesion characteristics and order prevalence are described. In the multivariable model, case birds were more likely to have been previously housed with a bird with mycobacterial disease involving the intestinal tract (odds ratio [OR] = 5.6, P < 0.01) or involving only nonintestinal sites (OR = 2.0, P < 0.01). Cases were more likely to have been imported into the collection than hatched at the ZSSD (OR = 4.2, P < 0.01). Cases were moved among ZSSD enclosures more than controls (OR = 1.1 for each additional move, P < 0.01). Findings will help guide future management of this disease for zoo bird populations.