Objective Identify the biological, social, and economic conditions influencing the knee height/stature index (KHSI) in growing individuals of Maya ancestry in the city of Merida, Yucatan, Mexico. Methods The hypothesis was that KHSI values would be lower in subjects with two Maya surnames. This was tested by analyzing the effect of a series of environmental, biological, and socioeconomic variables on stature and knee height (KH). Data were collected from 2008 to 2009 from 841 individuals (444 girls), 9 to 17 years of age, in Merida, Yucatan, Mexico. Ancestry was used as a proxy for genetics, and based on number of Maya surnames (2, 1, or none). The KHSI was calculated for all individuals. Multiple regression models were run to identify the variables that best explained variation in stature, KH, and KHSI. Results Ancestry negatively (P < 0.05) affected stature, but birth weight, crowding index, and mother's education level (MEL) were more significant (P < 0.01). Ancestry had no effect on KH and KHSI values, but birth weight and MEL had a significant effect. Individuals who had grown up in an adverse environment, in terms of MEL, had higher KHSI values. Apparently, lower leg length was proportionally longer than thigh length in the sample. Conclusions Growth measurements were more responsive to the studied environmental variables than to ancestry‐related genetic conditions. Genetic predisposition is, therefore, not the primary cause of short stature in this sample of Yucatec Mayas. Am. J. Hum. Biol., 2013. © 2013 Wiley Periodicals, Inc.