The use of crop varieties resistant or tolerant to insect pests or other stress factors is one approach in non-chemical crop-protection. Knowledge of the biochemical and molecular background of insect–plant interactions is a prerequisite for optimizing breeding for resistance. However, the resistance genes involved in plant–aphid interactions have so far only been identified and characterized in very few plant species. Our work aims to elucidate the molecular and biochemical mechanisms involved in resistance of apple trees, Malus domestica L. (Rosaceae), against its primary aphid pest, the rosy apple aphid, Dysaphis plantaginea (Passerini) (Homoptera: Aphididae), which is considered a serious economic pest of apple. Gene expression in both resistant and susceptible apple cultivars after infestation with rosy apple aphids was investigated by employing the cDNA-AFLP method (cDNA–Amplified Fragment Length Polymorphism). From approximately 12 500 cDNA fragments detected on polyacrylamide gels, 21 bands were apparently up- or down-regulated only in the resistant cultivar ‘Florina’ after aphid infestation compared to the susceptible cultivar ‘Topaz’ and/or mechanically wounded or non-infested leaves. These fragments were cloned, sequenced, and the pattern of gene expression for six fragments was subsequently verified by virtual Northern blots. Sequence comparisons of these fragments to GenBank accessions revealed homologies to already known genes, most of them isolated from Arabidopsis thaliana L. Among them, a putative RNase-L-inhibitor-like protein, a pectinacetylesterase, an inositol-phosphatase-like protein, a precursor of the large chain of the ribulose-1,5-biphosphate-carboxylase, and defence-related genes such as a vacuolar H(+)-ATPase subunit-like protein and an ADP-ribosylating enzyme were identified. The results are discussed in relation to a putative role of these genes in conferring aphid resistance in apple trees.