Chemiluminescence (CL) detection based on the horseradish peroxidase (HRP) catalyzed reaction of luminol with peroxide was investigated as a post-separation detection scheme for microchip-based capillary electrophoresis. An integrated injector, separator and post-separation reactor was fabricated on planar glass wafers. The fluorescein conjugate of HRP (HRP-FI) was used as a sample for optimization of the CL detector response. In devices etched 10 mu m deep, with an aluminum mirror integrated onto the backside of the detection zone to enhance collection efficiency, the detection limit, estimated at 3 standard deviations (SD) above background noise, for 1 nL injected sample plugs was 35 nM in HRP-FI. In devices etched 40 mu m deep, 8 nL plugs gave a detection limit of 7 nM. Separation and CL detection of the products of an immunological reaction of a F(ab')(2) fragment of the HRP conjugate of goat anti-mouse immunoglobulin G (IgG) with mouse IgG was performed on-chip. A linear calibration curve was obtained for the decrease in peak height of the HRP conjugate (53 mu g/mL) with increasing mouse IgG (0-60 mu g/mL). When microperoxidase was used as an internal standard, the R-2 value of a linear least-squares fit was 0.9867, and the relative errors in the slope and intercept were +/-5.8 and +/-1.3 %, respectively.