The science of genetics grew from a wish to relate the phenotype of an organism to its underlying genotype. The human genome was an interesting target for analysis but the early techniques used to study the genetics of simple organisms could not be adjusted to cope with its size or complexity. Recombinant techniques developed in the 1970's brought about a revolution in genetics as they allowed the analysis of complex DNA. As the pace of analysis grew, fresh techniques were developed to meet new challenges. In particular, highly informative marker systems have been used as landmarks in a variety of genetic and physical maps of the human chromosomes. In addition, yeast artificial chromosomes (YACs) have been developed as vectors with which to clone and propagate large fragments of human DNA. These advances lead to the evolution the Human Genome Mapping Programme (HGMP), which aims to prepare a genetic, physical and gene map of each human chromosome and to eventually elicit the entire sequence of human DNA. However, it was evident that some areas of the genome were considerably less well characterised than others and chromosome 3 was identified as one such region. This chromosome is therefore particularly interesting as a great deal remains to be learnt about the genes which map here. Two regions of interest on the chromosome have been selected for a YAC-based mapping analysis. The organisation of the Zeneca YAC library into gridded pools of YAC clones lends itself to screening with polymerase chain reaction (PCR) strategies. A collection of markers from a deletion on 3p13-p14 were used to test a new mapping concept 'YAC subpool mapping'. They were grouped and ordered on the basis of sharing common subpool identities based on the likelihood that markers which share the same subpool location will be found later to reside on the same YAC. This reduces the number of YACs requiring further characterisation to a minimum. This hypothesis was upheld as mapping and order information was obtained for the marker collection. However the subpool contigs were smaller than expected mainly because the deletion was larger than initially estimated. Although walking methods had been exploited to generate YAC contigs, new and improved techniques to characterise YACs were required if the aims of the HGMP were to be met. The selection of the best subset of YACs which can be used for further walking was streamlined into a rapid and efficient procedure using a combination of PCR and pulsed field gel electrophoresis (PFGE). Several important modifications were also made to the method for obtaining the terminal regions of YACs which are used for walking. The developments made in the mini-Vectorette method have a 99% success record with all of the YACs tested so far. Finally a new method, YAC panel strip hybridisation, was developed to allow rapid orientation of YACs and the identification of overlapping clones. Having developed better methods for the Identification and characterisation of YACs, these were applied to mapping the human chromosomal sub-band 3q27. In total, three YAC contigs of 17 YACs were prepared and 11 cosmid markers were mapped to the cloned material. In the course of this work one unstable YAC was identified and further characterised and three chimeric YACs were also detected. In addition new methods for the preparation of the sequenced tagged site (STS) markers from cosmids and Alu-PCR fragments using modifications of the mini-Vectorette method were also successfully used. As the ultimate goal of the HGMP is to generate an integrated genetic, physical and gene map of the human genome, methods to identify and map genes were applied to the 3q27 YACs. Expressed sequence tags (ESTs) for histidine-rich glycoprotein (HRG), alpha2-HS glycorotein (ASHG) and klninogen (KNG), all members of the cystatin superfamily of genes, together with human peroxisomal enoyl-CoA hydratase: 3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme (PEHHD) and a gene associated with Non-Hodgkins Lymphoma were all mapped to the 3q27 contigs. Using PFGE, CpG islands were also identified from the YACs as a screening method to identify those likely to contain genes. This data was also used to give a more accurate estimate of the physical size of the three 3q27 contigs. In total the contigs contain approximately 2.7Mb of cloned material from 3q27. Following the work described in this thesis, a new collection of methods and tools are available to begin work on hitherto poorly characterised regions of the human genome.