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Background: Small intestinal mucositis is a common side-effect following high-dose chemotherapy, causing patients to experience pain and abdominal complications often leading to extended stays in hospital. A biomarker to detect these small intestinal changes does not exist in clinical practice. This study aimed to assess the noninvasive 13C-Sucrose breath test (SBT) to detect small intestinal damage associated with mucositis in pediatric cancer patients having chemotherapy., Patients and Methods: Small intestinal function was assessed in 15 pediatric cancer patients and 26 healthy children. Subjects were studied for small intestinal permeability (SIP; lactulose/rhamnose), digestive and absorptive capacity (SBT; sucrose), and oro-cecal transit time (OCTT; lactulose), by ingesting two sugar drinks containing the respective sugars. Combined tests were carried out at baseline, day 1, day 3-5 and day 6-9, and in healthy individuals on two separate occasions. A total of 25 cycles of chemotherapy were assessed. Breath samples for the SBT were collected every 15 min for 3 h (expressed as % cumulative dose at 90 min (CD)), a 5 h urine collection for SIP and breath hydrogen determined every 30 min for three hours for OCTT., Results: Clinical mucositis occurred in seven of the 25 cycles of chemotherapy (28%). No significant difference was observed for SIP and OCTT. The SBT %CD at 90 min was significantly lower in the mucositis group compared to the unaffected group and controls at baseline (p<0.05). Patients who developed mucositis maintained a significantly lower %CD, for all test points (p<0.05) compared to the unaffected patients. In patients who developed mucositis the SBT was below the reference range of the controls at all time points., Conclusion: The findings show for the first time that it is possible to noninvasively detect and monitor gut damage associated with chemotherapy-induced mucositis in pediatric cancer patients.