We report on the development of a non-invasive instrument based on scanning confocal microscopy for tracking inherently fluorescent drugs and measuring spatial features in the anterior chamber of the eye. The new instrument incorporates all features of the initial instrument1 with the addition of fluorescence detection from within the anterior chamber of the eye. We have measured the diffusion of Fluorescein with high time resolution within a cuvette, an artificial eye and ex vivo porcine eyes. Results are be presented that demonstrate the capability of the instrument to accurately measure the concentration and the location of the fluorescent drug over a given period of time along the optical axis of the eye with an axial resolution of under 200 μm and temporal resolution of < 1s. We show that the instrument has high sensitivity and can measure concentrations of < 1μM/L of compounds having a quantum yield as low as 0.01 with high specificity for the compound of interest over competing background signals. The role of the instrument in assessing the efficiency of any inherently fluorescent ophthalmic drug as well as monitoring other medication that might produce fluorescent compounds in the eye will be discussed. We furthermore believe that the instrument might also be capable of monitoring certain bodily processes which have an impact on the compounds present in the eye.© (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.