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Background: The main manifestations of the functional constipation (FC) often described firstly by the disturbance of the colonic function, the colon transit time (CTT) is the main indicator, which can reflect the function of the colon motility. Aim: To investigate the usage of the radio-opaque markers (ROM) method in evaluating the colon transit function and the diagnosis of FC. Method: Using a simple and an optimal way of the (ROM) method to evaluate the whole and segmental colonic transit time (CTT) for 32 healthy subjects; and measuring the excretion rate (intestinal emptying) at a different time for 26 FC patients and 32 healthy subjects. Results: The total CTT for the healthy group was 20.31±11.00h, segmental transit time was 4.43±4.58h, 8.44±4.10h and 7.48±7.98h, respectively. The different genders were no obvious statistical significance (p>0.05). For the healthy group and the FC group which were done at four different times 36h, 48h, 60h, 72h, the excretion rate were statistically significant (p<0.01). The residual rate >20% during the 72h as a criteria, among of the 26 FC patients there are 19 patients showed a slow transit time; and the residual rate was 100% during 48h but residual rate was <20% during the 72h in the two FC patients. Conclusion: the radio-opaque markers method is an optimal and simple method and easy to be achieved, and having the accurate and effective evaluation of the colonic transit function, in particular the diagnosis of FC.