A multi-site fluorescence recording system provides simultaneous monitoring of cell activity in different brain regions of a freely moving animal. The system includes an electrical rotary joint that couples signals to and from an external data acquisition and control unit connected to a stator of the rotary joint, which releases twisting of the optical fibers connected to the animal. Electrical signals are coupled to one or more fluorescence stimulation/detection units on the rotor of the rotary joint. The fluorescence stimulation/detection units receive one or more connections from optical fibers that connect the stimulation/detection unit(s) to the different brain sites. The rotating stimulation/detection units include spectral filters to separate the excitation light from the fluorescence signal, light sensors (an image sensor or photodiodes) and excitation light sources.