Introduction. Inflammatory bowel disease (IBD) is characterised by recurrent inflammation of the intestinal mucosa, however the exact mechanism is unknown. Reactive molecules play a central role in the disruption of the mucosa increasing the permeability across the intestinal barrier, which may induce or sustain an immune response. Changes in detoxification of substances that causes epithelial damage may confer susceptibility to IBD. Hence, polymorphic enzymes involved in the detoxification processes may be risk factors of IBD. Methods. The two biotransformation enzymes microsomal epoxide hydrolase and N-acetyltransferase 2 were genotyped using TaqMan based Real-Time PCR in 388 patients with Crohn's disease (CD), 565 patients with ulcerative colitis (UC) and 796 healthy Danish controls. Results. No association was found between low microsomal epoxide hydrolase activity or slow N-acetyltransferase 2 acetylator status and IBD. An association between high activity of microsomal epoxide hydrolase and disease diagnosis before age 40 in CD with an OR of 2.2(1.1- 4.2) P=0.02) was found. No other phenotypic associations were found for the two enzymes and IBD, regarding age at onset, disease location, or severity of disease measured either as need for surgery or azathioprine treatment. Smoking was found to be a risk factor of CD (OR=1.8(1.4; 2.3) P<0.001), as opposed to current smoking being a protective factor regarding UC (0.7 (0.5-0.9) P=0.02) which is in agreement with previous findings in other study populations. Conclusion. Microsomal epoxide hydrolase and N-acetyltransferase 2 appear not to be important in susceptibility of IBD in the Danish population. Nor did we find convincing evidence of associations between the two polymorphic enzymes and phenotypic features in IBD. Smoking was found to be a risk factor of CD and a protective factor regarding UC. Being a complex disease, IBD are most likely dependent on an interaction between genetic and environmental factors.