Chimerism analysis has become a routine method to document engraftment and also for detection of residual disease. PCR-based procedures using STR analysis, especially commercially available multiplex assays, are frequently used. However, these assays have been optimized for forensic purposes and do not necessarily fulfil all needs for chimerism analysis. To improve these analyses, data on the level of informativity of STR systems in the context of chimerism analysis would be helpful. We evaluated 27 STR markers for their informativity in 203 patients and their HLA-matched related donors. These STRs included 18 from different multiplex kits, whereas nine were selected from the literature or STR databases. The STR profiles were ranked from Type 1 (not informative) to Type 5 (best suited for chimerism analysis). According to this ranking, the informativity of the STR systems was found highly variable, ranging from 4.4 to 49.0% Type 5 constellations. Among the most informative STRs were Penta E, SE33, D2S1338 and D18S51. Informativity of an STR was correlated with the degree of heterozygosity (r=0.86; P=0.0001), but not with the total number of alleles present. These data indicate that selection of suitable STR markers is important to improve diagnostics based on STR analysis.