A multi-channel optical detection system includes a base unit adapted to receive a multi-chamber assay cartridge having a plurality of reaction chambers loaded with a sample and an optical detection reagent, such as for example a fluorescence detection reagent, and an optical detection unit having a multi-channel optical block having a plurality of detection channels each with an associated light source, and an optic sensor. The optical detection unit is connectable to the base unit so that interrogation ports of the detection channels are optically aligned with optically transparent windows of the reaction chambers of a loaded cartridge. In an example embodiment, connecting the optical detection unit to the base unit initializes the optical detection process which includes activating the lights sources to direct an interrogating light beam into the reaction chambers to interrogate reaction products produced therein, and controlling the optic sensors to detect the optical responses from the interrogated reaction products in the reaction chambers. If a heating element is provided in the base unit, connecting the optical detection unit to the base unit may also trigger heating of the reaction chambers prior to initializing the optical detection process.