Barley seed dormancy is controlled by multiple genes that have a strong interaction with the environment. Lack of adequate dormancy results in pre-harvest sprouting in the field under wet weather conditions. On the other hand, too much dormancy has a detrimental effect in the malting house. There is only a very 'narrow window' of dormancy for malting barley. Harrington barley, which has been a dominant malting variety in the international market and widely used in Australia barley breeding programs, is highly susceptible to pre-harvest sprouting. A doubled haploid (DH) population derived from a cross of Chebec/Harrington was used to search for molecular markers linked with seed dormancy and pre-harvest sprouting. One major quantitative trait locus (QTL) was identified to control pre-harvest sprouting measured by alpha-amylase activity in barley grains, and could explain > 70% of the phenotypic variation. This QTL was located on chromosome 5HL and flanked by restriction fragment length polymorphism ( RFLP) marker CDO506 and simple sequence repeat (SSR) marker GMS1. The SSR marker (GMS1) linked with this QTL was further validated in a Stirling/Harrington DH population. A minor QTL on chromosome 2H accounted for 8% of phenotypic variation. Two QTLs for seed dormancy were located on chromosomes 2H and 5HL. The major QTL for dormancy coincided with the QTL for pre-harvest sprouting at chromosome 5HL and explained 61% of phenotypic variation. Since the presence of the Harrington allele at this locus favoured not only pre-harvest sprouting, but also increased malting extract, diastatic power, alpha-amylase, and free amino acid nitrogen, development of high malting quality varieties with pre-harvest sprouting tolerance would appear to be difficult.