Dr. Czaja's National Institutes of Health (NIH)-funded research attempts to understand the mechanisms of liver injury and hepatocyte death in order to develop new therapeutic approaches to prevent human liver failure. These investigations have defined signal transduction pathways that mediate liver injury from inflammatory factors such as the cytokine tumor necrosis factor and oxidants during toxin-induced liver injury, and regulate the development of steatosis and the progression to steatohepatitis in fatty liver disease. His laboratory first described the metabolism of endogenous cellular lipids through the lysosomal pathway of autophagy, and additional work in his laboratory has delineated functions for autophagy in both hepatocytes and macrophages that limit liver injury.

Dr. Czaja has held numerous positions, including associate editor and editorial board member of major scientific journals as well as chair or member on NIH study sections and national committees. He has served on the Governing Board of the American Association for the Study of Liver Diseases. He is an elected member of the Association of American Physicians as well as a Fellow of the American Association for the Study of Liver Diseases.