In this paper, we describe a capillary-based microfluidic device utilizing flow induced dispersion analysis (FIDA) for quantitative characterization of biomarkers. The microfluidic device is fabricated by micromilling technology and has incorporated buried optical fibers for light detection. The angle and distance between the fiber guiding the excitation light source and the fiber collecting fluorescent emission light were optimized to enhance signal-to-noise ratio (SNR) and limit of detection (LOD). The prototype achieves a LOD of 50 nM for the fluorescein indicator by using a low-cost Miniature Fiber Optic Spectrometer. The FIDA-based procedure employing fluorescein as the indicator and human serum albumin (HSA) as the analyte is carried out in the microfluidic device.