neural tube defects are the second most common birth defect of the central nervous system. the aim of this research is to design and optimise a novel detection system to analyse five markers that have been shown to be linked to neural tube defects. the developed detection system consists of three steps: an initial multiplex pcr, a hemi-nested multiplex pcr, and a multiplex sne-pcr using the abi prism® snapshot™ kit. the additional step of a hemi-nested pcr has been incorporated to increase the sensitivity and specificity of the test. by detecting all five markers simultaneously, the linkage between each of the mutations can be ascertained more rapidly than if detected independently. four different sample types were analysed, modern dna, experimentally degraded dna, medical specimens and archeological samples. the genotypes were successfully generated for all the samples except the archeological samples, where only partial genotypes were achieved. the designed detection system can be applied to archive medical specimens (biopsies, smears, and blood donor cards), archeological material, and other degraded samples. future applications of this technique can include medical screening, population mapping, association studies, familial pedigrees, and the study of the evolution of diseases. this developed three step methodology can be applied to the detection of other diseases and conditions.