Chert beds are intercalated in a Miocene sedimentary succession of the Niu Mountains, central Japan, which was deposited in very shallow water. The provenance of sediments was a volcanic suite from eruptions during back-arc spreading in the Sea of Japan. The cherts accumulated in a small lake underlain by lithic sandstone, and lithification was rapid and before deep burial. Much of the silica appears to be derived from extensive devitrification and weathering of volcanic ash and sediments nearby. X-ray diffraction analyses and microscopic observations reveal that the cherts consist of various types of chalcedony, microcrystalline quartz, and megaquartz of very low crystallinity indices. Transformation of chalcedony to megaquartz was common in the cherts. Scanning electron microscopic analysis shows that a chainlike alignment of micron-size silica spheres forms fibers of chalcedony. Morphological change and coalescence of the chalcedony fibers result in formation of crystalline quartz with numerous crocks and defects. The apparent crystalline quartz in the cherts has inner porous domains and small holes or pipes at the crystal surfaces. Rotation, movement, and rearrangement of the spheres seem to be as important as age effects and solubility of silica minerals.