A catheter-based fluorescence confocal microendoscope has been developed for in vivo imaging. The catheter in this system consists of a coherent fiber-optic imaging bundle, a miniature objective, and a focus mechanism. The proximal end of the catheter is coupled to a slit-scan confocal microscope so that high-resolution fluorescence images of cells and tissue microstructure can be viewed in real-time. The performance of the microendoscope is limited by the characteristics of the fiber bundle. The lateral resolution of the system is 1.8 microns and the axial resolution is 25 microns. The field of view is 430 microns. The maximum imaging depth, is around 200 microns below the tissue surface, but this depends on the tissue properties and wavelength range of operation. The slit-scan confocal microscope allows both gray-scale imaging at 8 frames per second and multi-spectral imaging. The frame rate in the multi-spectral imaging mode is determined by the number of spectral channels. The system has been demonstrated using topically-administered exogenous fluorescence dyes in excised tissues and in vivo animal models. A new catheter is under development with a maximum diameter of 3mm, which will allow it to be routed through the therapeutic instrument channel of a conventional clinical endoscope, making the device practical for routine clinical use.