Anthropometric assessment during pregnancy is a widely used, low-technology procedure that has not been rigorously evaluated. Our objective is to investigate fat mass distribution during pregnancy by examining changes in anthropometrics measures, in order to evaluate the reliability of these measures. An observational, longitudinal, prospective cohort study was performed in 208 pregnant women. Anthropometric measurements were taken following the ISAK protocol during the three trimesters and a generalized linear model for repeated measures was used to evaluate differences. Variability was assessed using the coefficient of variation, and Propagated Error (PE) was used to sum of skinfold thicknesses (SFT). SFT showed a general increase in fat mass during the three trimesters of pregnancy (∑SFT7 p = 0.003), and was observed in specific anatomical locations as well: arms (∑Arm SFT, p = 0.046), trunk (∑Trunk SFT, p = 0.019), legs (∑Leg SFT, p = 0.001) and appendicular (∑Appendicular SFT, p = 0.001). Anthropometric measures for skinfold thickness were taken individually during pregnancy and were reliable and reproducible during the three trimesters, which could help to prevent adverse pregnancy outcomes.