<p>In medical forensics, the detection of more than two alleles at a single locus is generally interpreted as a mixed sample or contamination. However, this can also indicate chimerism, in which an individual contains two or more distinct cell lines with different genomes. Multiple alleles at a single locus can be identified using short tandem repeat (STR) genotyping. In this study, we report a case of chimerism in a child, in which multiple alleles were detected at several loci during routine paternity testing. In particular, two alleles were detected at six loci with markedly uneven peaks, and three alleles were detected at 10 loci using different analysis kits. Analysis of additional samples from the father, mother, and child revealed that the three alleles were only present in the child’s blood. Comprehensive analyses of multiple data sets confirmed that the child had congenital chimerism. The findings of this study highlight the importance of conducting comprehensive evaluations of potential chimerism when multiple alleles are detected at a gene locus to ensure the accuracy and reliability of the results and improve the credibility of genetic evidence. After excluding other factors, the potential for chimerism should be acknowledged in legal practice to ensure accurate and reliable identification. Chimerism can be a major confounding factor, and unless professionals are aware of this condition, they may draw incorrect conclusions with serious ramifications for the individuals involved.</p>