Early-rearing salmonids in Ontario Ministry of Natural Resources (OMNR) fish hatcheries have been consistently affected by bacterial gill disease (BGD) (causative agent: Flavobacterium branchiophilum) for many years. Separate retrospective epidemiological investigations of BGD treatments at two OMNR fish hatcheries (Hatcheries A and B) for the 1999 production year were conducted using on-site hatchery records. Both investigations were carried out at the rearing unit-level, with early-rearing (<9 months of age) "tank-lot" as the unit of analysis to identify unique fish populations over time. Multivariable repeated measures logistic regression models were created for both hatchery datasets, controlling for lot-level and species effects. For Hatchery A, the species brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta) were significantly associated with BGD treatment, as well as lower water exchange rate, and higher feeding and mortality percentages during the 2 weeks previous to BGD treatment. At Hatchery B, the species brook trout (S. fontinalis) and splake (Salvelinus namaycush x S. fontinalis) were significantly associated with BGD treatment, as well as lower individual fish weights and treatment for BGD during the previous week. These results emphasize the importance of water quality, feeding rate, fish size and prior mortality on the development of BGD. Significant hatchery and species effects were evident, and future observational research on BGD must account for these factors in their design and analysis.