Background The MATRICS Consensus Cognitive Battery (MCCB) and proposed co-primary measures are gaining momentum as outcome measures in clinical trials, highlighting the need to evaluate their psychometric properties. The MCCB composite score has been proposed to be the optimal primary outcome measure, though its validity is unknown. This study aimed to evaluate the factor structure of the MCCB in a schizophrenia sample and determine whether its cognitive domains are separable. Methods 183 outpatients with schizophrenia or schizoaffective disorder completed a comprehensive test battery. Confirmatory factor analysis was used to test the factor structure of the MCCB; hierarchical regression then examined the relative contribution of individual cognitive variables to predict the MCCB factor scores. Finally, the relationships between the resulting factors and two performance-based measures of functional capacity were explored. Results A three-factor MCCB model representing processing speed, attention/working memory, and learning fits the data well and was an improvement over a unifactorial model. Symbol coding, spatial span, and visual learning were the most robust predictors for each of the three factors; symbol coding proved to be the best single predictor of overall cognitive performance. The three factors were also significantly related to a performance-based measure of everyday functioning but not a performance-based measure of social skills. Conclusions These analyses suggest that the six MCCB “domains” as constructed can be collapsed into fewer domains composed of multiple item scores; they also support the notion that impaired processing speed is a fundamental cognitive deficit in schizophrenia and that MCCB performance is related to functional capacity. Cognition and functional capacity measures require more research to determine if they differ.