The rate of particle clearance from the gills was assessed in healthy rainbow trout (Oncorhynchus mykiss), challenged with the formalin-killed bacterium Flavobacterium branchiophilum, as well as in fish with altered ventilation levels produced by varying the concentrations of dissolved oxygen (DO) in the water. The clearance of F. branchiophilum from the gills was quantified by means of an enzyme-linked immunosorbent assay. Fish held under normoxic conditions (DO = 9.5 mg/l) showed an initial rapid reduction in bacterial antigen, with 50% of the bacteria being cleared in the first 12 h after exposure, followed by slower clearance for the remaining bacteria; total elimination was achieved by 40 h. Fish with reduced ventilation rates (hyperoxia; DO = 25 mg/l) and elevated ventilation rates (hypoxia; DO = 4.5 mg/l) had significantly impaired particle clearance (r < 0.05), achieving only 60 and 20% reduction, respectively, at 72 h after challenge.