We describe the development of a micro total analysis system for the detection of ochratoxin A (OTA) in wine and beer. The OTA detection strategy is based on an indirect competitive ELISA detection by chemiluminescence with the integration of microfluidics with microfabricated amorphous silicon photodiodes fabricated on glass substrates [1] . The full lab-on-chip (LoC) assay is implemented on a prototype device for fully-automatic measurement and monitoring of photodiode signals and control of fluid handling. The device is composed of three peripheral control and measurement modules: a peristaltic pump, a fluid dispenser for fluid handling, and a multi-sensor data acquisition with custom transimpedance amplifier. A microcontroller interfaces the individual modules with a computer via USB communication. The analysis is run automatically and the results displayed through a PC controlled user interface. OTA was detected in wine and beer extracts down to 0.5 ng/mL.