Background Nutrition with antioxidant capacity can have important effects on the proinflammatory status of individuals. Fruit and vegetable consumption was been reported to influence proinflammatory gene expression. Patients with fructose/lactose intolerance represent a group of controlled dieters. The current study assessed the potential difference of proinflammtory gene expression between fructose/lactose intolerant patients and healthy controls. Methods In total 71 subjects were investigated. 17 fructose/ 35 lactose intolerant patients (in total n=52) were compared to healthy controls (n=19). Experimental determinations included anthropometry and gene testing. Psychometric and dietary assessment included BDI (Beck Depression Inventory), sociodemographic variables and 4-day food records. The mRNA was isolated from peripheral blood cells (PBC) and the gene expression concerning selected inflammatory markers (ICAM1, IL1R1, IL-6, TNFα, NFκB1) was assessed by quantitative realtime PCR. Data were evaluated by conducting correlation statistics and GLM multivariate. Tukey tests were used for post hoc group comparisons. Results After controlling for gender, age and depressive symptoms, fructose/lactose intolerant individuals still exhibited lower mRNA values of IL-6 (p<0.001) than healthy controls. No significant results were found for all the other inflammatory markers. Furthermore the analysis of 4-day food records revealed a significantly higher intake of beta carotene and fiber in fructose/lactose intolerant patients (p<0.001). Conclusion The observed lower levels of mRNA values of IL-6 in fructose/lactose intolerant patients suggest a beneficial effect of antioxidant food intake. An increased sensitivity in food selection caused by fructose/lactose intolerance might contribute to an improved anti-inflammatory status. Our results support the importance of new tools for the assessment of nutrient-gene interactions.