Clonality analysis is a critical tool for the diagnosis of suspect lymphoproliferative disorders. Amplification of the immunoglobulin and T cell receptor genes on genomic DNA from the suspect samples is followed by analysis of the PCR products to distinguish between polyclonal and clonal rearrangements. These analyses are based on electrophoresis in polyacrylamide gels after heteroduplex formation, or more frequently, GeneScan analysis is performed by capillary electrophoresis in automated DNA analysers, providing higher resolution and sensitivity. An alternative method for clonality analysis is the use of single-strand conformation analysis; however, this usually required labour intensive work with polyacrylamide gels and radioactive labelling. Within the EuroClonality group, we have developed a non-radioactive automated analysis based on capillary electrophoresis of single-strand PCR products that combines some of the benefits of heteroduplex and GeneScan analysis. This new method could be particularly suitable for challenging cases and could be implemented as an alternative to the more laborious heteroduplex analysis in standard gels in some instances.