Understanding the resistance mechanisms of plants against pests contributes to the sustainable deployment of plant resistance in Integrated Pest Management (IPM) programmes. The Mi-1 gene in tomato is the only one described with the capacity to provide resistance to different types of harmful organisms such as plant parasitic nematodes and pest insects, including the whitefly Bemisia tabaci MED (Mediterranean species). In this work, gene expression in the interaction of B. tabaci with susceptible tomato plants lacking the Mi-1 gene (cv. Moneymaker, compatible interaction), and with resistant plants carrying the Mi-1 gene (cv. Motelle, incompatible interaction) was studied using the oligonucleotide microarray technique. Both interactions were studied 2 and 12 days post infestation (dpi) of plants with adult insects. At 2 dpi, 159 overexpressed and 189 repressed transcripts were detected in the incompatible interaction, while these figures were 32 and 47 in the compatible one. Transcriptional reprogramming was more intense at 12 dpi but, as at 2 dpi, the number of transcripts overexpressed and repressed was higher in the incompatible (595 and 437, respectively) than in the compatible (71 and 52, respectively) interaction. According to the Mapman classification, these transcripts corresponded mainly to genes in the protein and RNA categories, some of which are involved in the defence response (signalling, respiratory burst, regulation of transcription, PRs, HSPs, cell wall or hormone signalling). These results provide a wealth of information about possible genes related to the resistance provided by the Mi-1 gene to B. tabaci, and whose role deserves further investigation.