The utility of dental calculus as a proxy for diet and mouth use is explored for the Middle Holocene Cis-Baikal region of Central Siberia based on two methods: a macroscopic analysis of severity and a microscopic analysis of particles within deposits. The study area was inhabited by two culturally and biologically distinct cultures, the Early Neolithic (EN) Kitoi culture (8,000 to 7,000/6,800 cal B.P.) and the Late Neolithic-Early Bronze Age (LN-EBA) Isakovo-Serovo-Glaskovo (ISG) cultural complex (6,000/5,800 to 4,000 cal B.P.), separated by a period of cultural transition marked by a cessation in formal cemetery use. Data were collected from four cemetery sites, two dating to the EN and two dating to the LN-EBA. Nonparametric testing of calculus severity revealed that, for adult males and juveniles, lakeshore populations displayed greater affinity to each other than to their contemporaneous cultural counterpart populations living along riverine systems in the Angara River Valley. Trends within the EN cemetery Shamanka II contrasted to the other cemetery populations, with noticeably larger deposits in anterior quadrants and significant sexual distinctions. The proportion of protein to carbohydrates consumed is known to influence calculus formation, but both cultural groups lived on a diet based predominately on meat sources so dietary ratios alone do not adequately explain the differences distinguished. A complex multifactorial model involving microregional differences in resources/environment, foraging patterns, individual variation, and dental wear patterns provides at least a partial explanation for the results observed. A wide range of particles were recovered during the microscopic analysis of calculus, albeit in low concentrations. The low starch grain counts were consistent with a diet based predominately on meats but still provide some of the first direct evidence for plant consumption in the Cis-Baikal, including possible plant processing by cooking or grinding based on damage evident on the grains. Other particles recovered may provide evidence of mouth use activities or palaeoenvironmental influences. Together, the two components of this analysis offer strong evidence that dental calculus is a useful tool for reconstructing hunter-gatherer lifeways but also highlight the limitations of conducting this type of research on previously excavated and potentially contaminated material.