A 3 mm catheter-based fluorescence confocal microscope has been developed for in vivo use. The catheter in this system fits through the therapeutic channel of a commercial endoscope. The catheter consists of a coherent fiber-optic imaging bundle, a miniature objective, and a focusing mechanism. The proximal end of the catheter is coupled to a slit-scan confocal microscope. Real-time images can be obtained of fluorescing tissue microstructures. The optical performance of the microendoscope is limited by the characteristics of the fiber bundle. The lateral resolution is 1.8 μm and the axial resolution is 25 μm. The field of view is 430 μm. The maximum imaging depth is 200 μm. The confocal microscope operates in both grayscale and multispectral modes. Images have been obtained of in vivo animal models and ex vivo human models. A portable confocal microscope system is under development for in vivo clinical evaluation.