Head smut is one of the most devastating diseases in maize, causing severe yield loss worldwide. Here we report identification and fine-mapping of a major quantitative trait locus (QTL) conferring resistance to head smut. Two inbred lines 'Ji1037' (donor parent, highly resistant) and 'Huangzao4' (recurrent parent, highly susceptible) were crossed and then backcrossed to 'Huangzao4' to generate BC populations. Four putative resistance QTLs were detected in the BC(1) population, in which the major one, designated as qHSR1, was mapped on bin 2.09. The anchored ESTs, IDPs, RGAs, BAC and BAC-end sequences in bin 2.09 were exploited to develop markers to saturate the qHSR1 region. The recombinants in the qHSR1 region were obtained by screening the BC(2) population and then backcrossed again to 'Huangzao4' to produce 59 BC(2:3) families or selfed to generate nine BC(2)F(2) families. Individuals from each BC(2:3) or BC(2)F(2) family were evaluated for their resistances to head smut and genotypes at qHSR1. Analysis of genotypes between the resistant and susceptible groups within the same family allows deduction of phenotype of its parental BC(2) recombinant. Based on the 68 BC(2) recombinants, the major resistance QTL, qHSR1, was delimited into an interval of approximately 2 Mb, flanked by the newly developed markers SSR148152 and STS661. A large-scale survey of BC(2:3) and BC(2)F(2) progeny indicated that qHSR1 could exert its genetic effect by reducing the disease incidence by approximately 25%.