Abstract Earlier studies have shown that acetaldehyde, the primary intermediate in the biological degradation of ethanol, interacts with enzymes and zymogens of the common coagulation pathway, prolonging prothrombin time and activated partial thromboplastin time (APTT), and that acetaldehyde-glycosaminoglycans (GAGs) mixtures synergistically prolong clotting times (Brecher, A. S. (2005). In Comprehensive Handbook of Alcohol Related Pathology. Vol. 3(93), pp. 1223–1244). In this study, the effect of acetaldehyde and GAGs upon Factor IXa, an intrinsic pathway enzyme, has been investigated. Individually, acetaldehyde, heparins of various molecular weights, dermatan sulfate, and chondroitin sulfates A and C affect Factor IXa, prolonging clotting time as measured by APTT. Pre-incubation of Factor IXa with a mixture of 22.3 mM acetaldehyde and heparin 17k, heparin 6k, dermatan sulfate, or chondroitin sulfate A additively prolongs clotting times, reflecting individual, unrelated molecular mechanistic effects. In contrast, a synergistic effect is observed at the 44.7 mM acetaldehyde level with heparin 17k, heparin 3k, chondroitin sulfates A and C, and dermatan sulfate, suggesting that acetaldehyde may cross-link with the enzyme and the GAGs, forming tertiary complexes, further influencing coagulopathy. These observations upon Factor IXa present a deeper dimension to the anticoagulation effect of alcohol on the coagulation cascade.