Developmental dyslexia is a learning disability that specifically affects reading acquisition. Cortical anomalies and gray matter volume differences in various temporal regions have been reported in dyslexic subjects compared with controls. However, consistency between studies is lacking. In the present experiments, we focused our structural analyses on the ventral occipitotemporal regions, defined by their functional response to visual categories. We applied a subject-by-subject functionally guided approach on a total of 76 participants (31 dyslexic children). Cortical thickness was estimated for each participant around his/her peak of specific functional activation to visual words, faces, or places. Results from two independent datasets showed a reduction in thickness in dyslexic children compared with controls in the region responsive to words, in the left hemisphere. Additionally, a gender-by-diagnosis interaction was observed at the same location, due to differences in girls only. To avoid the potential confound of reading level, we also contrasted dyslexic and control children matched for reading performance, and we observed a similar difference, although in a smaller extent of cortex. The present study thus provides the first account of a focal cortical thickness reduction in dyslexia in the subregion of ventral occipitotemporal cortex specifically responsive to visual words, when age, gender, and reading performance are taken into account.