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The addition of fiber is one of the most important dietary means to relieve constipation through lifestyle modification. Polydextrose (PDX) has been reported in several studies to increase fecal bulk, soften stools, and increase the number of defecations. However, there are few studies on the effect of PDX on colonic transit time (CTT). Therefore, the aim of this study was to demonstrate the effect of PDX on CTT and other aspects of gastrointestinal function during two weeks (Day 1 to Day 14), preceded by a 2-week run-in period (Day -14 to Day -1). A total of 192 adults who were diagnosed with functional constipation per Rome III criteria were recruited for the study. Participants were randomized equally into 4 groups (12 g, 8 g, or 4 g of PDX or placebo per day). The primary endpoint was CTT, assessed using radio-opaque markers and abdominal X-rays on Day 0, the baseline; and Day 15, the end of the intervention. Secondary outcomes that were measured using inventories were the patient assessment of constipation symptoms and quality of life, bowel function index, relief of constipation, bowel movement frequency (BMF), stool consistency, degree of straining, and proportion of bowel movements. Ancillary parameters and harms were also evaluated. The recruited population was not sufficiently constipated (e.g., baseline values for CTT and BMF of 42 h and 8.7 BMF/week, respectively). Despite this limitation, our results demonstrated an increased number of bowel movements when supplemented with PDX at a dosage of 12 g per day for 2 weeks. This dosage also consistently improved the secondary outcomes that were measured using inventories at Day 15, compared with the baseline. No serious or significant adverse events were reported during the study.