Bone loss is the most common systemic manifestation in inflammatory bowel disease (IBD). It is likely that this phenomenon is multifactorial and includes inflammation, malnutrition and glucocorticoids. Notwithstanding, large gaps remain in our knowledge of bone loss in IBD and the underlying mechanisms. Recent evidence implicating that high levels of gut-derived serotonin (GDS) are associated with bone loss via inhibition of osteoblastogenesis, could constitute a new explanation to the pathogenesis of bone loss in IBD. We, therefore, tested the hypothesis that GDS contributes to bone loss in IBD. In this study, we used a mouse model of spontaneous chronic colitis named Winnie, in which intestinal inflammation results from intestinal epithelial defect conferred by mutation in the Muc2 mucin gene. GDS levels in 15week Winnies were higher compared to age matched controls. We then investigated the detailed mechanism mediated by GDS using quantitative gene expression analysis of bone marrow mesenchymal stem cells ex vivo from 6 and 15week Winnies. We observed that the expression of GDS receptor gene Htr1b was similar in 6week Winnies compared to age-matched controls. In addition, we identified no significant change in gene expression of LRP5, CREB and FOXO1 in 6week Winnies as compared to controls. In contrast, significantly higher Htr1b expression was observed in 15week Winnies together with a significant decrease in the osteogenic genes LRP5 and CREB, and an increase in the anti-osteogenic gene FOXO1 as compared to controls. Also, we found β-catenin independent LRP5 down-regulation in Winnies compared to controls. In the light of our observations, we propose that high levels of GDS and increased activation of GDS-mediated signalling pathway could be partially responsible for bone changes in Winnies. In conclusion, these findings support the novel concept that high levels of GDS levels and activity can be a contributing factor in colitis-induced bone loss.