Fluorescent in situ hybridization (FISH) was used to quantify the ammonia-oxidizing populations within intact biofilm samples collected from a full-scale nitrifying trickling filter (NTF). Ammonia, nitrite, and nitrate concentrations were measured for aqueous samples taken in conjunction with biofilm samples at multiple filter depths. The ammonia removal capability of collected biofilms was evaluated by transferring the biofilms to laboratory batch reactors. Nitrate plus nitrite generation rates were calculated for the full-scale NTF and for the bench-scale reactors. Correlation coefficients for individual sampling events, calculated by simple linear regression of FISH signal area and nitrate plus nitrite generation rates for the full-scale NTF, ranged from -0.882 to 0.984. Correlation coefficients obtained for FISH signal area and nitrate plus nitrite generation rates for the bench-scale reactors ranged from 0.853 to 0.994 when using probe Nso190 and from 0.919 to 0.986 when using probe Neu23a. Occasional differences between the number of ammonia-oxidizing bacteria quantified by the probe Nso190 versus the NEU23a probe with depth suggest that genera other than Nitrosomonas are present in the NTF.