Exploratory factor analyses (EFAs) of the Comprehensive Trail Making Test suggested a possible two-factor solution that might better reflect the differences in Trails 1-3 and Trails 4 and 5 as opposed to a single Composite Index for the total standardization sample. The purpose of this study was to conduct a confirmatory factor analysis (CFA) of the two-factor structure with a subset of the standardization sample ages 18 or younger that had completed all five-trail tasks. The sample included 251 boys and 306 girls, ages 8-18, with a mean age of 12.76 (SD = 3.07). Data were collected across 16 states with representation from all regions of the USA. Standardized scores on each of the trails (1-5) tasks were considered. The results of CFA using M-plus indicated a good fit for the two-factor model, χ(2)(4) = 18.686, p = .0009, root mean-square error of approximation = 0.081, comparative fit index = 0.986 and standardized root-mean-squared residual = 0.021. A one-factor model was not supported. As suggested by the EFA in the manual, Trails 1-3 and Trails 4 and 5, while related, appear to be different in subtle ways that may be most meaningful in conjunction with evaluation of children with neurodevelopmental differences. Implications and possible explanations for this difference are discussed.