Significant improvements in the performance of a capillary electrophoresis (CE) microchip with an electrochemical detector are observed using a carbon nanotube (CNT)-modified working electrode. The CNT-modified electrode allows CE amperometric detection at significantly lower operating potentials and yields substantially enhanced signal-to-noise characteristics. The electrocatalytic detection is coupled to resistance to surface fouling and hence enhanced stability. Such advantages are illustrated in connection with several classes of hydrazine, phenol, purine, and amino acid compounds. Substantial minimization of surface fouling effects has been demonstrated in connection with the monitoring of phenol and tyrosine. Factors affecting the performance of the new CNT detector were assessed and optimized. CNTs from different sources are evaluated, and the effect of an anodic pretreatment is explored. The broad and significant catalytic activity exhibited by CNT-based CE detectors indicates great promise for a wide range of bioanalytical and environmental applications.