A retrospective whole-population survey was used to investigate putative risk factors for bacterial gill disease (BGD) in young hatchery-reared rainbow trout in North America. Three sets of analyses were done. The first analysis included as cases all of the hatcheries in which there was at least one outbreak of BGD during the 2-year study interval, regardless of location of the outbreak in the hatchery. The case group for the second analysis was limited to hatcheries for which the BGD outbreak occurred inside the hatch house. The case group for the third analysis was limited to hatcheries for which the BGD outbreak occurred outside of the hatch house. For the logistic regression that combined all cases of BGD (regardless of location of the outbreak), there was a significant association between mortality from bacterial gill disease and previous experience with BGD outbreaks (odds ratio (OR) = 10.1; 95% confidence interval (CI) = 5.6, 18.2), being a commercial trout hatchery (OR = 5.2; 95% CI = 2.6, 10.4), and being a hatchery with an annual salmonid fish production of > 250,000 fish (OR = 2.9; 95% CI = 1.5, 5.7). For BGD outbreaks that occurred in the hatch house, the presence of fish in the hatch house water supply significantly increased the odds of an outbreak (OR = 5.3; 95% CI = 2.2, 12.6), as did the use of ultraviolet radiation to disinfect the hatch house water (OR = 7.5; 95% CI = 2.2, 25.8), previous experience with bacterial gill disease (OR = 19.3; 95% CI = 7.9, 46.8), and being a commercial hatchery (OR = 7.7; 95% CI = 3.2, 18.6). The odds of a BGD outbreak outside of the hatch house was significantly associated with previous experience with BGD (OR = 4.3; 95% CI = 2.2, 8.6) and with being a hatchery with an annual salmonid fish production > 50,000 pounds (OR = 2.5; 95% CI = 1.2, 5.1).