Relationships between avian physiology and bacterial assemblages in the cloaca are poorly understood. We used molecular techniques to analyze cloacal swabs from pigeons that were subjected to two immunological manipulations: lysozyme supplementation and endotoxin challenge. From the swabs, we derived ecological indices of evenness, richness, and diversity of bacterial assemblages. Challenge led to changes in evenness that depended on supplementation. When analyzing these changes, we neutralized the effects of a possible statistical artifact by including the starting values as a covariate. Repeatability calculations suggested that swabbing reliably captured the evenness but not the richness or diversity of bacterial assemblages in the cloaca.