Polyacrylamide has been the matrix of choice for isoelectric focusing owing to the virtual absence of electroendosmosis in this medium. Certain inherent limitations associated with polyacrylamide have prompted some investigators to use low-electroendosmosis agarose for isoelectric focusing, but with limited success thus far. We have developed a method for isoelectric focusing in agarose for the classification of alpha 1-antitrypsin variants. Sera are applied directly to agarose gels containing a pH 4-5 ampholyte mixture, focused for less than 1 h, and directly immunofixed. Resolution of major bands is equivalent to polyacrylamide, and Pi M subtypes can be distinguished without the use of a separator. This application demonstrates the high resolution of isoelectric focusing in agarose, a more practical and convenient matrix than polyacrylamide.