In recent years, there has been tremendous interest in developing a complete, high-volume, DNA analysis system using microfabrication techniques. Key to the success of such systems, is the development of a high-resolution separation and detection system for analyzing DNA reaction products. Over the past decade, many researchers have demonstrated that micromachined fluidic devices are capable of performing many of the required functions of such a device. However, all of these devices rely on expensive external fluorescence imaging systems that may limit the realization of a low cost, miniature DNA analysis chip. We have developed an on-chip fluorescent detection system and used it to detect individual DNA bands migrating in a microfabricated electrophoretic device. Fluorescence-based detection of DNA bands is achieved by incorporating a highly sensitive photodiode beneath the electrophoresis channel along with a thin film optical filter deposited above the diode. A miniaturized detection system, with sensitivity comparable to macroscale detection systems, could accelerate the realization of integrated `lab-on-a-chip' systems.