Novel electrophoresis devices for protein and DNA separation and identification have been presented and studied. The new device utilizes a contact resistance change detection method to identify protein and DNA in situ. The devices were prepared with a microelectronic micromechanical system (MEMS) fabrication method. Three model proteins and six DNA fragments were separated by polyacrylamide gel microchannel electrophoresis and surface electrophoresis. The detection of the proteins or DNA fragments was accomplished using the contact resistance increase of the detection electrode due to adsorption of the separated biomolecules. Key factors for the success of these devices were the optimization of fabrication process and the enhancement of detection efficiency of the devices. Parameters, such as microchannel configuration, size of electrode, and affinity of protein or polyacrylamide gel to the microchannel sidewall and bottom surface were explored in detail. For DNA analysis, the affinity to the bottom surface of the channel was critical. The surface modification method was used to enhance the efficiency of the microchannel surface electrophoresis device. The adsorption of channel separated protein and DNA on the detection electrode was confirmed with the electron spectroscopy for chemical analysis (ESCA) method. The electrical current (I) from the protein microchannel electrophoresis was usually noisy and fluctuated at the early stage of the electrophoresis process. In order to remove the current perturbation, an amorphous silicon (a-Si:H) thin film transistor (TFT) was connected to the microchannel device. The self-aligned a-Si:H TFT was fabricated with a two-photomask process. The result shows that the attachment of the TFT successfully suppressed the current fluctuation of the microchannel electrophoresis process. In summary, protein and DNA samples were effectively separated and detected with the novel TFT-driven or surface microchannel electrophoresis device.