We present a miniature microelectromechanical systems-based dual-axis confocal microscope capable of spatially coregistered fluorescence and reflectance imaging at multiple wavelengths. This device has a 10 mm diameter scan head with a 2 mm diameter tip for convenient use during surgery to guide tumor resection. The microscope has an adjustable focal depth of 20-200 micrometers and is capable of imaging with an axial resolution of 9 micrometers and in-plane resolution of 4 micrometers over a field of view of 450×450 micrometers. Simultaneous two-color imaging of individual optical sections is achieved by using a pair of grating-prism assemblies to compensate for chromatic dispersion in the 2 mm diameter gradient index relay lens at the distal tip of the device. Experimental measurements of the axial response of the microscope, as well as two-color images of a reflective bar target and fresh mouse brain tissues, demonstrate the performance of our device and its potential for multicolor in vivo optical sectioning microscopy.