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Background Constipation is a common clinical symptom but its etiology remains unknown. The aims of the study are to discuss the relation between body mass index (BMI), motilin and the slow transit constipation (STC). Methods A total of 178 patients with STC and 123 healthy volunteers as controls were divided into three groups according to the BMI, group A (BMI 25). Fasting and one hour postprandial plasma motilin were measured and the results were analyzed. Results There was significant difference in the constituent ratio between STC patients and healthy controls (p < 0.05). The percentage of group A, B and C in STC patients was 49.4% (88/178), 23.0% (41/178) and 27.6% (49/178), respectively; and group A had a higher percentage. Plasma motilin of fasting and one hour postprandial in STC patients of group A was significantly lower than that of group B and C (p < 0.05), but there was no difference between group B and C (p > 0.05). There was no significant difference in the results of plasma motilin of fasting and one hour postprandial among the three groups of healthy controls (p > 0.05). Plasma motilin of fasting and one hour postprandial in STC patients of group A was significantly lower than those healthy controls of group A (p < 0.05). The same results of plasma motilin of fasting and one hour postprandial could be seen in group B and C, respectively (p < 0.05). Conclusions A higher proportion of low BMI sufferers was found in the STC patients. The reason may be related to the lower release of the plasma motilin.