Abstract We have conducted paleomagnetic and environmental magnetic analysis of a sediment piston core recovered from Lake Biwa, central Japan. Tephrochronology and AMS radiocarbon dating showed that this core covers the time period since about 40 kyr BP. The variation of paleomagnetic direction shows a good agreement with the PSV record for the last 10 kyrs from the deeper water site (BIWA SV-3; Ali et al., 1999), although the amplitudes are subdued probably due to the relatively lower accumulation rate at the shallower site. Inclination lows of the pre-Holocene interval are correlated to PSV records reported from the marine sediments off Shikoku and in the Japan Sea. In addition, the variation of magnetic mineral concentration reflects environmental changes during the last glacial period. It is suggested that the flux of fine-grained magnetite, probably associated with greater precipitation, was increased during interstadial periods. The variation of anhysteretic remanent magnetization is likely correlated to the Dansgaard-Oeschger (D-O) cycles recorded in Greenland ice cores. An apparent swing of the PSV curve is recognized at about 27 ka, but evidence for the Mono Lake excursion at 32 ka around the D-O events 6 and 7 is unclear. Combination of the detailed paleomagnetic record and the sub-Milankovitch climate cycles thus provides better resolution for understanding geomagnetic secular variation and polarity excursions in space and time.