Rat apolipoprotein E (apo-E) exists in plasma as four unique isoelectric forms (designated E-1, E-2, E-3, or E-4 from acidic to basic, respectively). We have examined the processes accounting for this polymorphism using intact rats or cultured rat hepatocytes. Intrahepatic precursors of rat apo-E were isolated and analyzed on isoelectric focusing gels. The primary translation product of rat liver apo-E mRNA focused as two isoproteins with more basic pI values than the isoproteins of plasma apo-E. The microsome-processed translation product also focused as two isoproteins having pI values corresponding to apo-E-4 and apo-E-3 isoproteins of plasma apo-E. Following a bolus injection of [3H]leucine into the portal vein, intrahepatic isoproteins corresponding to plasma apo-E-2 and apo-E-1 isoproteins were first detected in the rough endoplasmic reticulum (RER) and Golgi fractions, respectively. The apparent molecular weight of intrahepatic apo-E increased as it passed from the RER to the Golgi. Only the most acidic isoform, apo-E-1, of plasma apo-E was sensitive to neuraminidase treatment indicating that sialic acid residues are responsible, in part, for the polymorphism of rat apo-E. Using cultured hepatocytes, tunicamycin (1 microgram/ml) inhibited the incorporation of [3H]glucosamine into both molecular weight forms of apolipoprotein B but did not influence the synthesis, glycosylation (as measured by [3H]glucosamine incorporation), or secretion of apo-E. Tunicamycin-inhibited hepatocytes secreted the normal complement of apo-E isoforms including apo-E-1, thus confirming that apo-E-1 is not an N-linked glycoprotein. These results suggest that post-translational modifications involving both RER and Golgi-specific reactions contribute to the polymorphism of rat apo-E.