A novel and versatile optical reader for microfluidic platforms is presented. The reader includes a modular insertion port based on the lock and key concept for reproducible alignment with a miniaturized optical detection system comprising an interchangeable light emitting diode (LED) and a photodiode. The modular nature of the insertion port allows the use of microfluidic platforms in variable shapes and fluidic configurations. Three different analytical methodologies based on absorbance or fluorescence measurements were used to demonstrate the flexibility and reproducibility of the proposed experimental setup.