Slit-scanning geometries for confocal microendoscopy represent a compromise between acquisition rate and optical performance. Such systems provide high frame rates that freeze motion but recent Monte Carlo simulations show that scattered light severely limits the practical imaging depth for in vivo applications. A new multi-point scanning architecture for confocal microendoscopy has been developed. The new scanner is based on a relatively simple modification to the slit-scanning geometry that results in a parallelized point-scanning confocal microendoscope that maintains the high frame rate of a slit-scanning system while providing optical performance close to that of a single point scanning system. The multi-point scanner has been incorporated into an existing multi-spectral slit-scanning confocal microendoscope. The new confocal aperture consists of a slit and a rotating low duty cycle binary transmission grating, which effectively produces a set of continuously moving widely spaced illumination points along the slit. The design maintains the ability to rapidly switch between grayscale and multi-spectral imaging modes. The improved axial resolution of the multi-point scanning confocal microendoscope leads to significantly better confocal sectioning and deeper imaging, which greatly improves the diagnostic potential of the instrument.