Abstract: A set of over 3 million putative single Nucleotide Polymorphism (SNPs) are now available for disease association studies, eventually replacing the current RFLP and microsatellite (STRP) linkage analysis screening sets. Many different technological platforms are available for allelic discrimination and, among them, Taq Man chemistry employing 5’ nuclease allelic discrimination is one of the most widely diffused. Each Taq Assay employs two allelic specific probes for each SNPs, commonly VIC or FAM dyes. Although technological advancements in assay design and application allows monitoring SNPs at a high-throughput rate with this technology, the allele calling procedure of any single sample still requires the manual intervention of an expert operator for adjustment of SNP-dependent thresholds, signal selection, and quality revision. Usually the genotyping is calculated at the end of the amplification process resulting in an end point analysis. To enable the genotyping of multiple SNPs in several different samples we developed an algorithm for the automatic allele-calling from real time data.