The Comprehensive Trail Making Test (CTMT) is a relatively new version of the Trail Making Test that has a number of appealing features, including a large normative sample that allows raw scores to be converted to standard T scores adjusted for age. Preliminary validity information suggests that CTMT scores are sensitive to brain injury and demonstrate expected correlations with other neuropsychological tests, although the evidence also suggests that the factor structure of the CTMT may differ in children with brain dysfunction in comparison to the standardization sample. The present study addresses this matter by conducting a confirmatory factor analysis (CFA) of the CTMT in 382 children and adolescents. Of the 382, 191 were diagnosed with various forms of brain dysfunction, including 140 who had sustained a traumatic brain injury. The other 191 participants were healthy controls who were individually matched on age and gender to the clinical group with brain dysfunction. Results of the CFA indicated that for the clinical group, a 2-factor model composed of Simple Sequencing and Complex Sequencing/Shifting factors provided the best fit for the data. Although these 2 factors were also identified in the controls, differences in pattern of loadings were present. Results suggest that the presence of brain dysfunction may alter the factor structure of the CTMT in children and adolescents.