Fractionation of alkaline phosphatase isoenzymes and isoforms by isoelectric focusing is a simple procedure that resolves up to 17 fractions having alkaline phosphatase activity. The fractions are stable at 4 degrees C, and undergo only slight changes during repeated freeze-thaw cycles. Pretreatment with phospholipase-C or sialidase changes the isoelectric focusing patterns of alkaline phosphatase in serum; we recommend they not be used owing to the loss of information. We found that the alkaline phosphatase fractions provide diagnostic information in addition to that given by the common liver-function tests in patients with chronic liver diseases. Primary biliary cirrhosis and primary sclerosing cholangitis showed similar biochemical changes, but they are very different from alcoholic cirrhosis based on the common liver-function tests and the alkaline phosphatase isoform patterns obtained by isoelectric focusing. Analysis of the laboratory data using neural networks has some limited use in distinguishing chronic and chronic-active hepatitis of any cause. We have confirmed the tissue assignments made by Griffiths (Prog Clin Biochem 1989; 8:63-74) for the alkaline phosphatase fractions in liver as obtained by isoelectric focusing: Fractions 1a and 1b show a strong correlation with biliary diseases, and fractions 2, 3, and 4 show consistent increases in patients with primary disorders of hepatocytes; these fractions have good sensitivity for hepatocyte injury, but their specificity is limited. Fraction 10 may be a marker of activated T-lymphocytes; it was abnormal in most of our patients suggesting that it is a sensitive but non-specific test. Analysis of alkaline phosphatase by isoelectric focusing deserves further evaluation, because it may facilitate the diagnosis of certain chronic liver disorders and could be a supplement to the biopsy.