This paper describes the fabrication and evaluation of a chemically modified carbon ink microelectrode to detect thiols of biological interest. The detection of thiols, such as homocysteine and cysteine, is necessary to monitor various disease states. The biological implications of these thiols generate the need for miniaturized detection systems that enable portable monitoring as well as quantitative results. In this work, we utilize a microchip device that incorporates a micromolded carbon ink electrode modified with cobalt phthalocyanine to detect thiols. Cobalt phthalocyanine (CoPC) is an electrocatalyst that lowers the potential needed for the oxidation of thiols. The CoPC/carbon ink composition was optimized for the micromolding method and the resulting microelectrode was characterized with microchip-based flow injection analysis. It was found that CoPC lowers the overpotential for thiols but, as compared to direct amperometric detection, a pulsed detection scheme was needed to constantly regenerate the electrocatalyst surface, leading to improved peak reproducibility and limits of detection. Using the pulsed method, cysteine exhibited a linear response between 10-250 microM (r(2) = 0.9991) with a limit of detection (S/N = 3) of 7.5 microM, while homocysteine exhibited a linear response between 10-500 microM (r(2) = 0.9967) with a limit of detection of 6.9 microM. Finally, to demonstrate the ability to measure thiols in a biological sample using a microchip device, the CoPC-modified microelectrode was utilized for the detection of cysteine in the presence of rabbit erythrocytes.