Rodent models indicate that parenting shapes offspring outcomes by programming the hypothalamic-pituitary-adrenal axis response to stress and, ultimately, altering brain structure and function. The present study tested this hypothesis and explored possible timing-dependent associations in a longitudinal sample of children (N = 63). At Time 1 (M = 4.23 ± 0.84 years) and Time 2 (M = 7.20 ± 0.89 years), children completed parent-child interaction tasks and a laboratory stressor after which salivary cortisol samples were collected. At Time 2, children also completed a structural MRI. Analyses revealed timing- and region-dependent associations between early and concurrent parenting and cortisol reactivity and hippocampal subregion volumes. Moreover, greater negative parenting during early childhood predicted greater cortisol reactivity three years later, which, in turn, led to reduced left hippocampal tail volume. Findings suggest that the hippocampus is sensitive to environmental influences during early childhood, a result that parallels findings from rodent models.