The complex nature of inflammatory bowel disease (IBD) means that the exact nature of the biochemistry of the condition is extremely hard to categorise. This in turn leads to inaccuracies in diagnosis and a possible delay in treatment for many affected patients. This provided the impetus for the EU funded project GENETICS OF IBD to adopt a systematic approach to further elucidate the polygenic basis of the disease. The aim was to apply proteomic and genomic techniques on a mass scale with validated molecular abnormalities to be used as therapeutic targets. The team based at the University Hospital of Schleswig-Holstein in Germany specifically aimed to implement a system of high throughput genotyping of single nucleotide polymorphisms (SNPs). These would then form the basis of further research as an extensive integrated database incorporating some 2.3 million SNP genotypes during the lifetime of this research project. Obtained from public databases, details of mutations detected were typed into sibling pair families and triplets, if appropriate. High throughput TAQman assay was used in the typing of both in microtitre plates. The fixed layout achieved was one factor that determined the rapid processing of the samples along with the TAQman procedure itself. TAQman real-time polymerase chain reaction measures the accumulation of the product, not at the end-point of the PCR as is conventional, but at the exponential stages which makes the process inherently more rapid. The TAQman plates were read and imported into the integrated database established by the project. Coordinates were assigned to each patient from the 384 or 96 well plates. Given the code, a genotype could be assigned to each individual. Furthermore, a quality control was derived from the controls on each plate. To achieve a cost cut of a factor of ten during the project, multiplexed SNPlex for genotyping was implemented. This allows the simultaneous typing of 48 SNPs against one sample. This means that further research using this project's database and methods will have a competitive edge.