Background: Dendritic cells (DCs) are sentinels of the immune system and are known to play a key role in allergic responses. However, it is not clear how DCs that have been exposed to an allergen support Th2 type immune responses. It is possible that DCs from atopic individuals are inherently programmed to support allergic disease, or it is the exposure of dendritic cells to allergens that is key to the development of allergic sensitisation. Methods: We used 2D gel electrophoresis and MALDI mass spectrometry to compare the proteome of DCs from atopic and non-atopic individuals in both the resting state and after stimulation with the major house dust mite allergen Der p 1. Results: Our data show that unstimulated DCs from atopic and non-atopic individuals are very similar at the whole cell proteome level, showing few differentially expressed proteins. However, upon stimulation with Der p 1, a number of additional proteins are differentially expressed, and of these several were of potential relevance to Th2 cell differentiation and the allergic response, including GTP-binding regulatory protein Gi alpha-2, frabin and cathepsin D. Conclusion: Whilst there are inherent differences between DCs from atopic and non-atopic individuals, it seems that exposure to allergen plays a key role in differential expression of proteins by these key immune cells. Further studies should now focus on establishing the biological relevance of these proteins as biomarkers in house dust mite allergy and their role in allergen induced Th2 cell differentiation.