Chagas' disease is caused by the protozoan parasite Trypanosoma cruzi and commonly modelled in inbred mice. Susceptibility of mouse strains to experimental infection varies considerably. We quantified parasite tissue burdens in resistant and susceptible strains by real time PCR and applied a backcross strategy to map the genomic loci linked to susceptibility in inbred mice. Resistant B6D2F1 mice were backcrossed with susceptible C57BL/6 mice, and 46 of a total 192 offspring died after infection. Their genomes were scanned with microsatellite markers. One region on chromosome 17 was significantly linked to susceptibility, while another on chromosome 5 was suggestive of linkage.