INTRODUCTION: Assessment of specific mRNAs in human samples is useful in characterizing disease. However, mRNA in human stool has been understudied. RESULTS: Compared to controls, infected stools showed increased transcripts of IL-1β, IL-8 and calprotectin. mRNA and protein concentrations correlated for IL-8, but not for calprotectin. DISCUSSION: Stool mRNA quantification offers a potentially useful, noninvasive way to assess inflammation in the gastrointestinal tract, and may be more sensitive than EIA. METHODS: We purified fecal RNA from 46 children infected with Campylobacter jejuni, Escherichia coli O157:H7, Salmonella spp. or Shigella sonnei and 26 controls and compared the proportions of IL-1β, IL-8, osteoprotegerin and calprotectin mRNA between groups using qRT-PCR. We determined the concentrations of calprotectin, IL-8 and osteoprotegerin by enzyme immunoassays in cognate specimens.