Background: Pre- and/or probiotics can cause changes in the ecological balance of intestinal microbiota and hence influence the microbial metabolic activities. In the present study, the influence of oligofructose-enriched inulin (OF-IN), Lactobacillus casei Shirota (LacS) and Bifidobacterium breve Yakult on the colonic fate of NH₃ and p-cresol was investigated. Methods: A randomized, placebo-controlled, cross-over study was performed in 20 healthy volunteers to evaluate the influence of short- and long-term administration of OF-IN, LacS, B. breve and the synbiotic LacS + OF-IN. The lactose-[¹⁵N, ¹⁵N]-ureide biomarker was used to study the colonic fate of NH₃. Urine and faeces samples were analysed for ¹⁵N-content by combustion-IRMS and for p-cresol content by GC-MS. RT-PCR was applied to determine the levels of total bifidobacteria. Results: Both short- and long-term administration of OF-IN resulted in a significantly decreased urinary p-cresol and ¹⁵N-content. The reduction of the urinary ¹⁵N-excretion after short-term OF-IN intake was accompanied by a significant increase in the ¹⁵N-content of the faecal bacterial fraction. However, this effect was not observed after long-term OF-IN intake. In addition, RT-PCR results indicated a significant increase in total faecal bifidobacteria after long-term OF-IN intake. Long-term LacS and B. breve Yakult intake showed a tendency to decrease the urinary ¹⁵N-excretion, whereas a significant decrease was noted on p-cresol excretion. Conclusion: Dietary addition of OF-IN, L. casei Shirota and B. breve Yakult results in a favourable effect on the colonic NH₃ and p-cresol metabolism, which in the case of OF-IN, was accompanied by an increase in total faecal bifidobacteria.