ObjectivesGlobally, Indigenous women and young children disproportionately face increased nutritional risks, which may have serious adverse health consequences. In Botswana, data is limited on the health and nutritional status of the San People, an Indigenous minority group primarily living in the Ghanzi District. This cross-sectional study aimed to assess the prevalence of anemia and undernutrition among San women and young children in Ghanzi District. MethodsWe recruited 367 mother-child pairs (women 15–49 years and children 6–59 months) from San households from nine randomly selected areas. A capillary blood sample was collected, and weight and height were measured in both mothers and children. Hemoglobin (Hb) concentration was measured using a hemoglobinometer (HemoCue, AB). As per global recommendations, Hb concentrations were adjusted for altitude, smoking (in women), and ethnicity. ResultsFifty-six % (n = 205/367) of women self-reported smoking in any form (rolled cigarettes or snuffing). Overall, adjusted anemia prevalence was 12% in non-pregnant women (Hb < 120 g/L), 26% in pregnant women (Hb < 110 g/L), and 42% in children (Hb < 110 g/L); but ranged widely based on the controversial factor of whether or not adjustments for ethnicity were applied (range of 6–26%, 22–30% and 35–68% prevalence, respectively). Thirty-nine % (n = 133/344) of non-pregnant women and 52% (n = 12/23) of pregnant women were underweight (BMI < 18.5 kg/m2). In children 6–23 months, 41% were underweight (weight-for-age z-score < -2SD), 13% were wasted (weight-for-height z-score < -2SD), and 65% were stunted (height-for-age z-score < -2SD); in children 24–59 months 57% were underweight, 13% were wasted and 66% were stunted. ConclusionsThe high prevalence of smoking among women, underweight status among pregnant women, and anemia, stunting, and wasting among children were of the highest public health concern and should be addressed in future health and nutrition programming. These findings will inform and guide targeted nutrition and health policies for the San People and potentially motivate more research with other Indigenous groups. Funding SourcesInternational Development Research Centre (Doctoral Research Award), Botswana International University of Science and Technology (Ph.D. Fellowship), and University of British Columbia (Public Scholar Initiative).