This paper reports on the strategy being used to study chickpea (Cicer arietinum) quantitative trait loci (QTL) conferring resistance to the necrotrophic fungal pathogen Ascochyta rabiei. The three chickpea linkage groups (LG), harbouring six QTL conditioning resistance against A. rabiei, were compared with the most comprehensive chickpea map (W-Ca-LG) and to the orthologous pseudochromosomes of the legume model plant Medicago truncatula. QTL1 was located in the subcentromere region of the chickpea W-Ca-LG3 (chromosome C) and on the short arm of the M. truncatula pseudochromosome 7. QTL2 and QTL3 were located on the long arm of the W-Ca-LG8 (chromosome H) and on the short arm of the M. truncatula pseudochromosome 5. QTL4, QTL5 and QTL6 were located in the subcentromere region of the W-Ca-LG4 (chromosome B) and in a similar location of the M. truncatula pseudochromosome 1. To further delimit the genomic regions where the QTL were located, 25 legume expressed sequence tags (ESTs), which were shown to be upregulated in resistant chickpea accessions challenged with A. rabiei, were selected and BLASTed against M. truncatula genome sequences using a chromosome visualisation tool. Eleven of the 25 ESTs were mapped in silico on the nine M. truncatula pseudochromosomes with 1–4 copies. The association of mapped ESTs with chickpea resistance to A. rabiei requires further characterisation.