Centimeter- to decimeter-scale rhythmical alternation of dark and light layers is common in siliceous rocks of the middle Miocene Onnagawa Formation of northern Japan. The siliceous rocks may also show micrometer-scale laminae considered to be varves. Dark layer frequency shows meter-scale cyclic variation with dominant spectral peaks of approximately 10, 5.4, 3.4, 2.3, and 1.6 m. For these, a varve-tuned average sedimentation rate of 139 mu m/yr yields periods of 72, 39, 24, 17, and 12 kyr, respectively. A sedimentation rate of 100 mu m/yr, which is within the range of biostratigraphically calculated rates, yields 100, 54, 34, 23, and 16 kyr, respectively. Considering the uncertainty in the estimation of the average sedimentation rate, these values are in relatively good agreement with orbital eccentricity, obliquity, and precessional cycles, respectively. Bottom water oxygenation levels deduced from the lamina preservation index are in phase with the frequency variation of dark layers, suggesting that it is also controlled by orbital cycles. Mineral and chemical analyses suggest that the siliceous rocks are mainly composed of biogenic (diagenetic) silica, terrigenous detritus, dolomite, and organic matter with minor amounts of carbonate fluorapatite. The dark colors are due to detritus and organic matter. Thus, alternation of dark and light layers and variation in the frequency of dark layers reflect compositional variation. Mass accumulation rates [MARs] of biogenic silica and terrigenous detritus are calculated from the average thickness of a lamina couplet, dry bulk density and chemical composition of individual samples. At the level of centimeter to decimeter layers, MAR of detritus is nearly constant, whereas MAR of biogenic silica varies by a factor of 2. On the other hand, MAR of detritus shows meter-scale variation, with amplitudes as high as a factor of 10, which is in phase with frequency cycles of dark layers, whereas MAR of biogenic silica does not show significant meter-scale variation. Compositional variation represented by dark and light alternation and frequency cycles of the dark layers are a result of the interplay of centimeter- to decimeter-scale (10 (super 2-3) years) variation in MAR of biogenic silica and meter-scale (10 4 years) variation in MAR of detritus. The latter could be related to global sea-level oscillation caused by orbital cycles.