Four different detection systems were compared for evaluation of polymerase chain reaction (PCR) amplified immunoglobulin heavy-chain gene rearrangements in acute lymphoblastic leukemia (ALL) and non-Hodgkin's lymphoma (NHL) of B-cell lineage. In 63.0% of the fragments detected by ethidium bromide stained agarose gel electrophoresis (Agarose-EtBr) the sensitivity was insufficient to separate the specific clonal population from the background of normal B cells. Using polyacrylamide gel electrophoresis (PAGE), PAGE combined with single-strand conformation polymorphism (PAGE-SSCP) and PhastGel-SSCP (Phast-SSCP) analysis with silver staining, the resolution was improved and the majority of the inconclusive amplicons were elucidated. However, Phast-SSCP displayed a slightly higher detection level compared to PAGE and PAGE-SSCP. According to our findings PAGE-SSCP and Phast-SSCP were superior to agarose-EtBr and PAGE in detecting new emerging clones and clonal evolution.