This dissertation describes the design and implementation of an immunoassay platform based on micron-scale magnetic beads. We target the diagnosis of infectious diseases in developing countries, where small, inexpensive, and automated tests are required. Conventional sensor technologies, such as Giant Magneto-Resistors (GMRs), have excellent sensitivity but are expensive and difficult to integrate with other circuitry. The system presented here is built around a CMOS sensor chip and uses standard manufacturing techniques present in the electronics industry. CMOS technology can provide high integration levels at comparatively low cost, but also suffers from some performance challenges. In this work, design strategies and calibration techniques are presented to achieve adequate performance from the CMOS sensor. The resulting system reliably detects the presence of magnetic beads on the sensor surface, enabling a method for detecting biological substances. This method is benchmarked against a pervasive assay technology, the Enzyme-Linked Immunosorbent Assay (ELISA). Sera from 12 patients infected with the dengue virus were tested with both platforms, and a high correlation in results was found.