NOD2, a cytosolic receptor for the bacterial proteoglycan fragment muramyl-dipeptide (MDP), plays an important role in the recognition of intracellular pathogens. Variants in the bacterial sensor domain of NOD2 are genetically associated with an increased risk for the development of Crohn disease, a human chronic inflammatory bowel disease. In the present study, global protein expression changes after MDP-stimulation were analysed by two-dimensional polyacrylamide gel electrophoresis of total protein extracts of human cultured cells stably transfected with expression constructs encoding for wildtype NOD2 (NOD2 ^wt) or the disease-associated NOD2 L1007fsinsC (NOD ^SNP13) variant. Differentially regulated proteins were identified by MALDI-TOF MS peptide mass fingerprinting and MALDI MS/MS. The limited overlap in the responses of the NOD2-overexpressing cell lines to MDP included a downregulation of Heat shock 70 kDa protein 4. A complex pro-inflammatory program regulated by NOD2 ^wt that encompasses a regulation of key genes involved in protein folding, DNA-repair, cellular redox homoeostasis and metabolism was observed both under normal growth conditions and after stimulation with MDP. Using the comparison of NOD2 ^wt and disease-associated NOD2 ^SNP13 variant, we have identified a proteomic signature pattern that may further our understanding of the influence of genetic variations in the NOD2 gene in the pathophysiology of chronic inflammatory bowel disease.