Despite therapeutic advantages, double-donor (DD) HSCTs present technical problems for molecular chimerism (CHM) monitoring. These DD chimeras contain three matched DNAs, so that the genomes of donor(s) and recipient often share the same alleles. In the STR assay, shared recipient/donor alleles are common and have identical physico-chemical properties. As a consequence of the latter, they co-migrate in the same band ('shared peak'), which prevents measuring each allele separately. Without individual allelic measurements, the direct calculation of the chimeric recipient/donor DNA ratio is precluded. This is the first study to document and systematically examine these problems. Its goal was to provide a validated framework for accurate, routine monitoring based on a stepwise analytic paradigm for approximating percent CHM (%CHM) from shared STR-alleles. Analysis of STR-DNA from DD loci showed that at least four of six alleles were typically shared. Despite such extensive allelic sharing, we show how simple arithmetic procedures can be applied for standardized calculation of %CHM based on peak measurements. Criteria for selecting loci suitable for such analysis are provided. Validation of the computational results required analyzing 18 'informative' loci with pre-established reference values for %CHM. In all cases, the results for %CHM, calculated from peak measurements, were +/-5% of the reference value. The conclusions of the study are as follows: (1) Multi-donor chimeras, with shared alleles, can be accurately and simply analyzed within the usual limits of STR measurement error; (2) by examining these various facets of DD CHM analysis, this novel study has provided a basis for standardized, routine quantitative monitoring using the STR/VNTR assay.