Amplified fragment length polymorphisms (AFLPs) produced with EcoRI and PstI both in combination with MseI restriction enzymes have been studied in the parents of four barley mapping populations. Averages of 15.9 and 18.7 polymorphic products per assay were produced for the EcoRI/MseI and PstI/MseI combinations, respectively. There was some evidence of interaction between cross combinations and restriction enzyme combinations, with PstI/MseI generating relatively more polymorphic products than EcoRI/MseI in the Blenheim x E224/3 cross combination, the least polymorphic of the four. Three hundred and ninety-eight AFLP products, using both restriction enzyme combinations, were generated in a doubled haploid population of 68 lines produced from the Blenheim x E224/3 cross. These were added to existing marker data for the cross to study the effects of incorporation of AFLPs produced by different restriction enzyme combinations upon genetic maps. Addition of the AFLP data resulted in greater genome coverage, both through linking previously separate groups and extensions to other groups. This increase in coverage appeared to result from AFLPs sampling some different regions of the genome compared to RAPDs and RFLPs, as the map distances spanned by the RAPD and RFLP linkage groups were similar with and without incorporation of AFLPs. There was also evidence that the EcoRI and PstI restriction enzymes sampled different regions of the genome. The revised maps were used in scanning for QTLs controlling a subset of 12 economically important traits measured in the cross. Overall, the QTLs accounted for an average of 53 per cent of the phenotypic variation for the characters. Positive and negative alleles were present in each parent for each character, apart from hot water extract corrected to 1.5 per cent nitrogen (HWEc). Several regions of the genome appeared to be involved in the control of several characters, notably chromosome 2, the denso locus on chromosome 3, the short arm of chromosome 5 and chromosome 7. Although there was considerable similarity to previous results of QTL mapping for the subset of characters, the greater genome coverage afforded by the inclusion of the AFLPs revealed some new QTL locations.