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We determined stunting, wasting, and obesity frequencies in a total 1092 2-to-12 year old Baka Pygmy children from anthropometric and health data gathered in 34 villages in the Djoum-Mintom region in southeastern Cameroon in four health campaigns in 2010 and 2017–9. We compare these to the WHO Child Growth Standards, Amazonian Tsiname growth references for inter-population comparisons and the study population itself. Population-specific growth charts were constructed using GAMLSS modelling. Our results show that Baka children have one of the highest global rates of stunting relative to the WHO child growth standard with 57.8% for 2-to-12 year olds and 64% and 73% for 2-to-4 year old girls and boys, respectively. Frequencies of wasting, overweight, and low BMI were low at 3.4%, 4.6% and 4.3%, respectively, for 2-to-12 year olds. Underweight was at 25.5%, in the upper range for sub-Saharan Africa. Edemas indicated rare severe malnutrition (0.3%). Uncertainties in age estimation had dramatic effects on the reliability of estimated individual z-scores but distributions of z-scores were robust at a population level. In the context of the recent evidence for genetic adaptation of the Pygmies’ small stature to the tropical forest environment we argue that WHO child standards for weight and BMI are applicable. However, standards for height are clearly not adequate for Pygmy people. To achieve UN Sustainable Development Goals, we recommend that Pygmy specific growth standards are developed for the various, genetically differing Pygmy tribes.