The Swedish Apheresis Registry is a National Quality Registry and performing intercenter comparisons can be done as one task. The purpose of this study was to evaluate differences in adverse effects (AE) associated with plasma exchange (PE) for the development of best practice. Six hundred and twenty reports of AE related to a total of 12,461 apheresis procedures performed during 1996-2002 were analyzed, and eight Swedish university hospital centers that reported AE every year were compared. About 70% of all PE in Sweden were performed in centers that also reported AE. During this period, there was no change in the proportion of PE procedures with AE, but there was a decrease in the frequency of prematurely interrupted procedures (2.1% to 1.3%, P = 0.003). The mean frequency of moderate and severe AE was 5%. Adverse effects were more common when PE was performed in patients with Guillain-Barré syndrome (GBS; 10%) or thrombotic thrombocytopenic purpura-hemolytic uremic syndrome (TTP-HUS; 8%) than in patients with macroglobulinemia/hyperviscosity syndromes (2%). In the eight centers, there was a four-fold difference in AE between the centers with the highest and the lowest frequency. The frequency of AE in GBS, TTP-HUS and macroglobulinemia/hyperviscosity syndromes differed four-fold, while the frequency of specified symptoms differed more than four-fold. The indications and the choice of substitution fluids could explain some of these differences. The results of the study have initiated changes in practice. The identification of significant intercenter differences in the frequency and symptoms of AE has started improvement in current PE practices.