This article reviews advances over the last 5 years in microfluidics and microchip electrophoresis techniques for detection of clinical biomarkers. The various advantages of miniaturization compared with conventional benchtop methods for detecting biomarkers have resulted in increased interest in developing cheap, fast, and sensitive platforms. We discuss the development of applications of microfluidics and microchip electrophoresis for analysis of various clinical samples for pathogen identification, personalized medicine, and biomarker detection. We highlight the advantages of microfluidics platforms over conventional methods that make them an attractive future diagnostic tool. We also discuss the versatility and adaptability of this technology for analysis of various biomarkers, including lipids, small molecules, carbohydrates, nucleic acids, proteins and cells. Finally, we conclude with a discussion of areas that need to be improved upon to move this technology towards routine clinical and point-of-care applications.