According to recent publications, one of the most promising methods of DNA analysis is that of capillary electrophoresis on a microchip. Many companies give much attention to the development of microchip tech-nologies and instruments for rapid analysis of biological substances. The main trends found in the development of microchip devices and systems include fabrication of multichannel instruments, integration of auxiliary ele-ments on a microchip, incorporation of microchip devices into analytical instruments (high-resolution micro-scopes, mass spectrometers, etc.). One of the problems in methods development for DNA analysis based on mi-crochip technology is the choice and synthesis of the separation matrix for efficient fragmentation. The paper presents the results of investigations on synthesis of poly(dimethyl acrylamide) with prescribed properties. The data obtained from electrophoretic separation of a mixture of DNA molecular weight markers on a glass micro-chip with different characteristics of the separation medium are discussed.