Purpose: Alcohol Use Disorder (AUD) is associated with dysfunction across cognitive and affective functional domains. Dimensionality reduction methods, such as exploratory factor analysis (EFA) can provide a comprehensive view of AUD-related deficits across functional domains. The overall aim of this project is to use EFA to examine a latent factor structure of a large, multidimensional data set, and to compare men and women on factor scores as a function of their history of AUD. Participants: One hundred and twenty-two adult volunteers were recruited from Boston, Massachusetts for this collaborative study with Boston University. The sample comprised sixty (33 women, age = 52.5 ± 11.5) abstinent individuals meeting AUD diagnostic criteria, and sixty-two (29 women, age = 50.4 ± 13.6) demographically matched control participants. Design/Methodology/Approach: EFA with direct oblimin rotation was used to reduce dimensionality of thirty-six cognitive and affective measures, including executive functioning, social perception, personality, mood, and drinking motivation. Plausibility and viability of the resultant factor structure was carefully considered. Resulting factor scores were used to test for group and sex differences in 2 x 2 ANCOVAs, controlling for age. Factors scores were used as predictors of Alcohol Use Disorder Identification Test (AUDIT) scores in linear regressions. Results: The EFA found a 4-factor solution best fit the data. The factors of fluid reasoning and cognitive functioning composed a cognitive domain, and negative affect and incentive salience composed an affective/motivation domain. Women had higher levels on the cognitive functioning factor than men, but this was true only in the AUD group. Relative to control participants, the AUD group had higher levels of negative affect and incentive salience, with AUD women showing marginally higher levels of negative affect than AUD men. Linear regressions found that only the affective domain significantly predicted harmful drinking patterns as measured with AUDIT. Conclusions: These results confirm accounts of women with AUD experiencing more affective dysregulation than men. The predictive relationship found between the affective domain and AUD status further highlights the importance of considering affective domains in AUD research and treatment. Better cognitive functioning in AUD women opposes previous studies and needs replication.