We are proposing a novel design for a module with depth of interaction (DOI) capability for gamma rays by measuring the pulse-height ratio of double-sided Multi-Pixel Photon Counters (MPPCs) coupled at both ends of a scintillation crystal block. Thanks to newly developed monolithic MPPC arrays consisting of 4×4 channels with a three-side buttable package, the module is very thin and compact, thereby enabling less dead space between each module when arranged into a fully designed gantry. To demonstrate our concept of a DOI measuring technique, we first made a 1-D crystal array consisting of five Ce-doped Gd3Al2Ga3O12 (Ce:GAGG) cubic crystals measuring 3×3×3 mm3 in size, separated by a layer of air. When the light signals output from both ends are read with the MPPCs, the position of each crystal is clearly distinguished with a spatial uncertainty of 0.48±0.03 mm. For 3-D measurements, we then fabricated three different type arrays: [A] 4×4×4 matrix of 3×3×3 mm3 pixels, [B] 5×5×5 matrix of 2×2×2 mm 3 pixels, and [C] 10×10×10 matrix of 1×1×1 mm3 pixels, with each pixel divided by a BaSO4 reflector in the 2-D direction and by a layer of air in the DOI direction. We demonstrated that the 3-D position of each Ce:GAGG pixel was clearly distinguished when illuminated by 662 keV gamma rays uniformly. Average energy resolutions of 9.8±0.8 %, 9.8±0.9 %, and 13.2±1.7 % were obtained for types A, B and C, respectively. These results suggest that our proposed method is simple and offers promise in achieving 1 mm 3-D spatial resolution for future medical imaging, particularly in positron emission tomography (PET).