Recent research indicates that mesenchymal stem cells (MSCs), known for their anti-inflammatory and anti-infectious properties, could be a promising alternative for treating inflammatory diseases such as inflammatory bowel disease (IBD). This study examined how MSCs and their derivatives, when cocultured with interleukin-1 (IL-1)-stimulated Caco-2 cells, affect the expression of genes related to inflammation, microbes, and apoptosis. In the experiment, Caco-2 cells were exposed to 10 ng/mL of IL-1 for 24 h. MSCs were sourced from human bone marrow, adipose tissue (AD-MSC), and menstrual blood. These MSCs and their conditioned medium (CM) were then cocultured with the IL-1-induced Caco-2 cells. After 48 h, gene expression levels were analyzed using real-time PCR, and the data were statistically evaluated using -tests, -Mann-Whitney, and Tukey's post hoc analyses. The results indicated that IL-1 at 10 ng/mL was the optimal concentration for inducing Caco-2 cells with the highest viability and minimal damage. Among the MSCs tested, AD-MSCs were the most effective in regulating gene expression. Specifically, AD-MSC treatment significantly reduced the mRNA expression of TNF- and IL-1, both of which are crucial in sustaining inflammatory responses ( ≤ 0.05). This study concludes that AD-MSCs have superior effects compared to other MSC sources in modulating genes associated with inflammation, antibacterial effects, and apoptosis in an in vitro model of IBD using Caco-2 cells.