Breastfeeding during infancy is associated with a range of short- and long-term health benefits. We examine whether breastfeeding in the first 2 months of life is associated with structural markers of brain development in infants from the general population. This study was embedded within the Generation R study. Cranial ultrasounds were obtained at approximately 7 weeks post-natal age. The diameter of the gangliothalamic ovoid, corpus callosum length, ventricular volume and head circumference were measured. Maternal reports of breastfeeding were obtained at 2 months of age. We examined associations in relation to current breastfeeding practices (exclusively breastfed, n = 318, breast- and bottle-fed, n = 119, and bottle-fed, n = 243). Analyses were adjusted for head size and relevant covariates. Secondary analyses were conducted for breastfeeding history (exclusively breastfed, n = 318, breast- and bottle-fed, n = 281, and never breastfed, n = 81). Exclusive breastfeeding was associated with more optimal brain development compared with babies who were bottle-fed or never breastfed. Results were most consistent for gangliothalamic ovoid diameter. Larger gangliothalamic ovoid diameters were evident in babies who were exclusively breastfed compared with bottle-fed babies [difference between means (95% confidence interval) = 0.21(0.02, 0.39), P = 0.02]. Smaller ventricular volume and larger head circumference were also found for exclusively breastfed babies. Breastfeeding was not significantly associated with corpus callosum length. Maternal reports of breastfeeding are associated with more mature brain development within the first 2 months of life. Results are most consistent for gangliothalamic ovoid diameter, a subcortical structure rich in docosahexaenoic acid. Findings also pointed to non-specific neural developmental advantage for exclusively breastfed babies.