Objective: We conducted a secondary analysis of baseline data from a recently completed pharmacological pilot clinical trial among 30 veterans with alcohol dependence and posttraumatic stress disorder (PTSD). This trial included baseline measures of alcohol use biomarkers, both indirect (carbohydrate-deficient transferrin, GGT [g-glutamyltransferase], mean corpuscular volume, AST [aspartate aminotransferase], alanine aminotransferase) and direct (ethyl glucuronide, ethyl sulfate), as well as neurocognitive measures (Trail Making Test parts A and B, Hopkins Verbal Learning Test-Revised, Balloon Analogue Risk Task, Delay Discounting Task). Methods: Two regression models were estimated and tested for each neurocognitive measure (dependent measure). The first model included the alcohol use biomarker alone as the predictor. The second model included the alcohol use biomarker along with the following 3 additional predictors: Beck Depression Inventory, Clinician-Administered PTSD Scale, and receiving medications. Results: In both models, the indirect biomarkers, such as GGT and AST, significantly predicted performance on the Hopkins Verbal Learning Test-Revised %Retention. GGT alone significantly predicted performance on the Trail Making Test part A. Conclusions: Indirect alcohol use biomarkers may have a specific role in identifying those veterans with alcohol dependence and PTSD who have impaired cognitive performance. However, direct alcohol use biomarkers may not share such a role.