The infant brain and gut microbiome both develop rapidly in early infancy. Growing evidence indicates that the gut microbiome plays a critical role in shaping neurodevelopment early in life, possibly through effects on brain regions involved in affective, interoceptive, and sensory processing. This study used magnetic resonance imaging (MRI) and whole genome sequencing of fecal samples to examine associations between the gut microbiome and brain structures in infants at 2 weeks of age. We identified significant relationships between specific gut microbiome characteristics and brain volumes in key regions involved in affective, sensory, and interoceptive processing. Our most consistent findings were associations between gut microbiome and insula volume, suggesting that the insula may be particularly sensitive to gut microbiome influences during the neonatal period. Specifically, a significant negative association between insula volume and the abundance of Veillonella was observed. Alpha diversity (Shannon) and functional pathways were also related to insula structure. Enterobacter was negatively associated with thalamus volume. These findings contribute to the growing evidence of a developing gut-brain axis, highlighting links between the gut and brain as early as 2 weeks of age. Future research should investigate the mechanisms by which specific microbial features impact neurodevelopment by way of the insula, as well as explore the potential long-term implications of these early relationships on sensory, interoceptive, and affective processing, and behavioral outcomes.