Alpha‐1‐antitrypsin (α1AT) deficiency in its most common form is caused by homozygosity for the α1AT mutant Z gene. This gene encodes a mutant Z secretory protein, primarily synthesized in the liver, that assumes an abnormal conformation and accumulates within hepatocytes causing liver cell injury. Studies have shown that mutant α1ATZ protein molecules form unique protein polymers. These Z protein polymers have been hypothesized to play a critical role in the pathophysiology of liver injury in this disease, although a lack of quantitative methods to isolate the polymers from whole liver has hampered further analysis. In this study, we demonstrate a quantitative α1ATZ polymer isolation technique from whole liver and show that the hepatocellular periodic acid‐Schiff–positive globular inclusions that are the histopathological hallmark of this disease are composed almost entirely of the polymerized α1ATZ protein. Furthermore, we examine the previously proposed but untested hypothesis that induction of α1ATZ polymerization by the heat of physiological fever is part of the mechanism of hepatic α1ATZ protein accumulation. The results, however, show that fever‐range temperature elevations have no detectable effect on steady‐state levels of intrahepatic Z protein polymer in a model in vivo system. In conclusion, methods to separate insoluble protein aggregates from liver can be used for quantitative isolation of α1ATZ protein polymers, and the effect of heat from physiological fever may be different in vivo compared with in vitro systems. (HEPATOLOGY 2005;41:160–167.)