Objective: Ascertain whether there are differences in the anthropometric measurements of at-term neonates in a rural population and an urban population at 3 400 m altitude. Material and methods: Descriptive population study of healthy at-term neonates in the Adolfo Guevara Velasco National Hospital (HNAGV) in Cusco and in the Huanoquite Health Center (CSH), [both at 3 400 m altitude in Peru], between 2005 and 2010. Measures of central tendency were calculated, the averages were compared with a Student’s t-test, the final model was adjusted by neonatal sex, and the odds ratios (OR) and corresponding confidence intervals (CI95%) were calculated to estimate the strength of association between small for gestational age (SGA) infants (according to weight under P10 and ponderal index [PI]) in mothers who live in the Huanoquite district and those who gave birth in the CSH. Results: In the HNAGV and the CSH, 372 and 368 neonates were studied, respectively. The average maternal age was 31.7 and 27.0 years; previous pregnancies, 2.4 and 3.4; miscarriages, 0.4 and 0.0; live births, 1.0 and 2.3 (p<0.001); and weight, height and PI, 3 311.8 g, 49.5 cm, 2.73, and 3,008.9 g, 48.4 cm, 2.66, respectively (p<0.001). The weight, height, and PI for the two centers were, after adjusting for sex and by gestational age bracket: (37-38 weeks) 3,185.1 g, 49.18 cm, 2.67, and 3,009.8 g, 48.5 cm, 2.64; (39-40 weeks) 3 385.9 g, 49.9, 2.73, and 3 051.8 g, 48.6 cm, 2.66; (41-42 weeks) 3 461, 6 g, 50.2 cm, 2.73, and 3,072.2 g, 49.1 cm, and 2.6, respectively (p<0.001). The OR of SGA births in the CSH was 3.52 (2.4-5.1) according to weight and 2.05 (1.3-3.1) according to PI, compared to birth in the HNAGV. Conclusion: The weight, height, and PI of infants born in the CSH were lower than those born in the HNAGV, and the OR of SGA births was 3,52 according to weight and 2,05 according to PI, respectively.