The objective of this study was to identify influences on longitudinal changes in autonomic function during pregnancy. We studied 195 low-income Peruvian women who were subjects in a randomized controlled trial of zinc supplementation and fetal neurobehavioral development. Maternal cardiorespiratory status and electrodermal activity were assessed at 20, 24, 28, 32, 36, and 38 weeks' gestation over a 50-min session. At baseline (10-16 weeks), and at 28 and 36 weeks' gestation, mass and height, arm and calf circumferences, and skinfold thicknesses were assessed, and blood was taken to measure hemoglobin, hematocrit, and plasma zinc concentration. Measures of heart period (HP), respiratory period (RP), respiratory sinus arrhythmia (RSA), skin conductance level (SCL), and mean arterial pressure (MAP) were analyzed using longitudinal models. Having a hemoglobin concentration <10.5 g.dL-1 at 28 weeks was associated with shorter HP and RP and lower RSA, and change in hemoglobin from baseline to 36 weeks was associated with decreased SCL. Further, 3 measures were associated with variation in fat or fat-free mass in the calf; RSA was negatively associated with changes in calf muscle area over pregnancy, while changes in calf fat area were positively associated with MAP and SCL. Variability in autonomic function during the second half of pregnancy is associated with hematologic status and changes in lower limb body composition across pregnancy.