The electrophoretic mobilities and catalytic rates of individual molecules of bovine intestinal alkaline phosphatase were determined in CHES and borate buffers of identical pH using a capillary electrophoresis based method. Both properties were found to be heterogeneous. In the presence of CHES, the mobility and rate were found to be −1.9 ± 0.2 × 10−9 m2 V−1 s−1 and 9.8 ± 7.4 × 104 min−1 ( N = 38), respectively. In the presence of borate, the mobility and rate were found to be −6.9 ± 0.5 × 10−9 m2 V−1 s−1 and 2.0 ± 1.3 × 104 min−1 ( N = 41), respectively. The means and variances for both properties were found to differ significantly between the two buffers. The difference in average mobility was attributed to an increase in negative charge caused by borate complexing with the carbohydrate moieties attached to the enzyme. The difference in variance was attributed to heterogeneous complexation with borate due to heterogeneity in the glycosylation. The differences in mean values for the catalytic rate were attributed to the inhibitory effect of borate and the difference in variance may suggest that the KI of this binding may also be heterogeneous.