This paper is concerned with development and optimization of a microchip system for biochemical analysis using a CCD-based fluorescent detector with temperature control of multiple samples in microreactors using Peltier elements. The topology of microchip injection ports was optimized along with the surface modification conditions to achieve simultaneous 3-5 μL samples introduction into microreactors of 250 nL. Surface passiva-tion was performed to improve biocompatibility of the microreactors. Thermocycling characteristics of the sys-tem were obtained and the real-time PCR was performed in 14 minutes for 10**4 initial DNA copies. The system was capable to monitor the kinetics of the biochemical reaction of catecholamines with the fluorogenic dye NBD-F and optimization of reaction conditions (temperature, pH) was performed.