A deep-focus three-dimensional endoscope based on a compact compound-eye camera called TOMBO (thin observation module by bound optics) with polarization filters and polarized illuminations is presented. TOMBO is a very compact multi-camera system, which is composed of a single image sensor, a lens array, and a crosstalk barrier. Features of TOMBO are compactness of the camera system, and additional functionality achieved by attaching optical filters to lenses. In this paper, to enhance surface or deep structures of biological tissues selectively, polarization filters, which are parallel and vertical to the polarized illumination, respectively, are attached to a part of lenses. To achieve extended depth of focus, a wavefront coding (WFC) technique based on the spherical aberration is introduced. A prototype TOMBO with 3x3 lenses and a 2.2-μm-pixel color CMOS image sensor was fabricated. Depth estimation and superresolution with the WFC technique are demonstrated. Enhancement of surface or deep structures is also verified theoretically and experimentally.