The potential use of single nucleotide polymorphisms (SNPs) for genetic mapping and medical diagnostics would require reliable and economical methods for high-throughput SNP genotyping, as the methods in use today are laborious and expensive. Scorpion primers (PCR primers with a fluorescent probe region attached to the 5' end) provide a new method for detection of PCR products. Their unimolecular mechanism of probing brings substantial advantages over other common fluorescent PCR detection methods, especially when the Roche LightCycler™ thermocycler is employed. Scorpions have been optimised for PCR detection tests on ABCC7 loci (cystic fibrosis), showing reliability for the discrimination of single nucleotide polymorphisms. Novel intramolecular TaqMan® 'intrataq' probes have also been designed and used in PCR reactions involving SNP discrimination in locus W1282X of the ABCC7 gene. The 'intrataq' probes have been shown to perform better than their intermolecular counterparts in PCR reactions carried out on the Roche LightCycler™ thermocycler. The possibility of development of a high-throughput SNP genotyping method using libraries of generic short probes has also been investigated.