Obstacles and possible solutions for the application of microchip capillary electrophoresis in quantitative analysis are described and critically discussed. Differences between the phenomena occurring during conventional capillary electrophoresis and microchip-based capillary electrophoresis are pointed out, with particular focus on electrolysis, bubble formation, clogging, surface interactions, injection and aspects related to the power supply. Current drawbacks are specified and improvements for successful quantitative microchip capillary electrophoresis are suggested.