Conventional PCR-SSP, which is based on an agarose gel-based read-out, has the disadvantages of time-consuming post-PCR steps and low potential for automation. The aim of our study was to sort out these drawbacks by establishing a fluorescence-based PCR-SSP system for HLA-C. The assay relies on the sequence-specific identification of amplicons with individually labeled probes that are cleaved during successful PCR by the 5'-3' exonuclease activity of the Taq-DNA Polymerase. The oligonucleotides are labeled with a unique and spectrally resolvable fluorescent reporter dye at the 5' terminus (FAM or TET) and a common quencher dye at the 3' terminus (TAMRA). In case of amplification, the reporter escapes from the quenching control caused by the physical separation of the dyes, resulting in a significant increase of the reporter fluorescence. This allows simultaneous and differential detection of the specific HLA (FAM) and internal control (TET) product. The HLA-C fluorotyping information is based on the individual reporter fluorescence released by 18 PCR primer mixes. Using this method, we analyzed 145 samples previously typed with conventional PCR-SSP and found a concordance rate of 100%. Furthermore, fluorotyping revealed quantitative results that may indicate the presence of homozygosity by high signal intensities. This provided extra protection not to miss new alleles which are not amplified by the current primer mixes. These features as well as the capability of high sample throughput and the possibility of automation makes fluorotyping an attractive tool for PCR-based HLA typing.