Biogenic Silica (BSi) has been one of the most important proxies for determining the palaeoclimate from Lake Baikal over glacial-interglacial cycles. Concentrations (calculated through a 1% Na2CO3 wet-alkaline digestion) at a site in the north basin, however, reveal consistently low values during MIS 3 compared to greater than tenfold changes in diatom concentrations and biovolumes from c. 53.3-51.5 kyr BP. With similar glacial trends present at other low sedimentation sites, we suggest that significant amounts of BSi are removed from diatoms during glacials due to a relative increase in diatom dissolution at the sediment-water interface. This contrasts with existing results from other, higher sedimentation, sites such as those within the Selenga Delta which display a strong relationship between diatoms and BSi. Site selection is therefore essential when searching for Heinrich and other glacial millennial-scale events in Lake Baikal, and we recommend that both BSi and diatom concentrations be calculated together in future studies.