The goal of the present study was to examine differences in cortical thickness, cortical surface area, and subcortical volume between bilingual children who are highly proficient in two languages (i.e., English and Spanish) and bilingual children who are mainly proficient in one of the languages (i.e., Spanish). All children (N = 49) learned Spanish as a native language (L1) at home and English as a second language (L2) at school. Proficiency of both languages was assessed using the standardized Woodcock Language Proficiency Battery. Five-minute high-resolution anatomical scans were acquired with a 3-Tesla scanner. The degree of discrepancy between L1 and L2 proficiency was used to classify the children into two groups: children with balanced proficiency and children with unbalanced proficiency. The groups were comparable on language history, parental education, and other variables except English proficiency. Values of cortical thickness and surface area of the transverse STG, IFG-pars opercularis, and MFG, as well as subcortical volume of the caudate and putamen, were extracted from FreeSurfer. Results showed that children with balanced bilingualism had thinner cortices of the left STG, left IFG, left MFG and a larger bilateral putamen, whereas unbalanced bilinguals showed thicker cortices of the same regions and a smaller putamen. Additionally, unbalanced bilinguals with stronger foreign accents in the L2 showed reduced surface areas of the MFG and STS bilaterally. The results suggest that balanced/unbalanced bilingualism is reflected in different neuroanatomical characteristics that arise from biological and/or environmental factors.