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It is known that different genes are expressed during ontogeny; however, it is unclear how variation in that expression is associated with changes in growth patterns. The objective of this study is to assess how genetic variation in fetal morphology changes with ontogeny in baboons. Longitudinal measures of the head and femur (60 to 180 days gestation) were available for 892 pregnancies. We used a genetic model that allowed both the genetic and environmental variances (cr% and cr|) to change with age and estimated genetic and environmental correlations (pG and pE) between measurements at different ages. The results indicate a significant increase in the genetic variance for biparietal diameter and femur length but not for head circumference and fronto-occipital diameter. The pG estimates for all measures decreased as the age between measures increased from 0 to 120 days, indicating that different groups of genes are expressed early in gestation and late in gestation. The pE estimates dropped rapidly from 1 to 0 for all measures, indicating temporally localized environmental influences on fetal growth. Thus fetal morphometries are significantly heritable and those genes that influence them show age-specific expression during ontogeny.