We present a modified multi-spectral configuration of a slit-scanning confocal microendoscope that provides higher spectral resolution in a fully automated interface. Tissue fluorescence signal is directed through a dispersive element that spreads the spectral information across the CCD camera mapping spectral information perpendicular to the confocal slit. The dispersive element may be chosen to meet the specific requirements defined by the user. Our current system uses a BK7 prism with a 45° wedge angle and a 20mm diameter clear aperture. The prism is shifted from the optical axis allowing automated switching from grayscale (beam on-axis) to multi-spectral (beam off-axis) imaging by tilting a computer controlled mirror. The system records over a spectral range of 450nm to 750nm. The minimum resolvable wavelength difference varies from 2.1nm to 8.3nm over the spectral range. The lateral and axial resolution of the system is approximately 3μm by 30μm, respectively, and is the same for both grayscale and multi-spectral imaging modes. Multi-spectral imaging results from ex-vivo tissues are presented.