INTRODUCTION: Recently there has been significant progress in research on the pathogenesis of inflammatory bowel diseases (IBD). AIM: Our study aimed to assess selected markers of bacterial translocation in children with IBD in relationship to disease activity. MATERIAL AND METHODS: Lipopolysaccharides (LPS) - markers of bacterial translocation - and proinflammatory cytokines - interleukin (IL)-8, IL-12 and tumor necrosis factor (TNF) alpha - were assessed in the serum of 27 pediatric IBD patients at the outbreak of the illness and then 1 and 3 months after the introduction of the treatment. The analyzed markers were taken once in 6 healthy children in the control group. RESULTS: Serum TNF-alpha and LPS concentrations were significantly higher in IBD patients than in the control group (1.74 vs. 0.83 ng/ml and 21.83 vs. 10.26 pg/ml, p < 0.05). In the study group, clinical and laboratory activity mediators significantly decreased during 3 months of the treatment. All proinflammatory cytokines decreased, but significant down-regulation was observed only in relation to IL-12 (129.21 vs. 82.98 pg/ml, p < 0.05) in CD and IL-8 (32.72 vs. 20.97 pg/ml, p < 0.05) in UC patients. TNF-alpha levels decreased but did not reach values as in healthy children, while LPS levels increased in both groups. CONCLUSIONS: IL-12 in CD and IL-8 in UC could be non-invasive markers of reduced inflammation during IBD in children. Improvements in clinical status and reductions in systemic inflammatory markers do not necessarily mean complete cessation of the inflammatory cascade. The elevated TNF-alpha and LPS levels found in patients in early remission may be a marker of subclinical inflammation.