Procalcitonin appears to be an early and sensitive marker of bacterial infection in a variety of clinical settings. The use of levels of procalcitonin to predict infection in children undergoing cardiac surgery, however, may be complicated by the systemic inflammatory response that normally accompanies cardiopulmonary bypass. The aim of our study was to estimate peri-operative concentrations of procalcitonin in non-infected children undergoing cardiac surgery. Samples of serum for assay of procalcitonin were obtained in 53 patients at baseline, 24, 48, and 72 hours following cardiac surgery. Concentrations were assessed using an immunoluminetric technique. Median concentrations were lowest at baseline at less than 0.5 nanograms per millilitre, increased at 24 hours to 1.8 nanograms per millilitre, maximized at 48 hours at 2.1 nanograms per millilitre, and decreased at 72 hours to 1.3 nanograms per millilitre, but did not return to baseline levels. Ratios of concentrations between 24, 48 and 72 hours after surgery as compared to baseline were 6.15, with 95 percent confidence intervals between 4.60 and 8.23, 6.49, with 95 percent confidence intervals from 4.55 to 9.27, and 4.26, with 95 percent confidence intervals between 2.78 and 6.51, respectively, with a p value less than 0.001. In 8 patients, who had no evidence of infection, concentrations during the period from 24 to 72 hours were well above the median for the group. We conclude that concentrations of procalcitonin in the serum increase significantly in children following cardiac surgery, with a peak at 48 hours, and do not return to baseline within 72 hours of surgery. A proportion of patients, in the absence of infection, had exaggerated elevations post-operatively.