Stem canker (blackleg) caused by Leptosphaeria maculans is a widespread disease of Brassica napus. In contrast, most Arabidopsis thaliana accessions are highly resistant. Hence, novel material derived from symmetric and asymmetric somatic hybrids between B. napus and A. thaliana was utilised in a screen for L. maculans resistance. Initially, both cotyledon and adult-leaf resistance traits were transferred from A. thaliana to B. napus. In later generations the two traits segregated and cotyledon resistance was lost. The adult-leaf resistance was investigated with respect to genome localisation and protein expression. Analyses of remaining A. thaliana DNA in resistant plants showed co-segregation between adult-leaf resistance and chromosome-3 molecular markers. Resistant offspring from asymmetric hybrid plants that contained fragments of chromosome 3 were studied in more detail. Two regions at positions 9.8-10.4 Mbp and 18-19.5 Mbp, where several defence-related genes are located, were identified. A proteomic approach was taken to further investigate genes involved in the defence interaction. Forty eight hours after inoculation with L. maculans, only a few proteins, such as glycolate oxidase, were identified as differentially expressed in the resistant line compared to B. napus, despite the presence of additional A. thaliana chromosomes. The plant materials described in the present study constitute a new genetic source of L. maculans resistance and are currently being incorporated into B. napus breeding programmes.