Background: Quercetin is known for its vast pharmacological activities in recent years. It has shown beneficial effects in animal models of colitis. Purpose: The effectiveness of quercetin in human IBD is limited. Results from these pre-clinical studies indicate an opportunity for developing anti-colitic polyphenol treatments. Methods: In the present study. Quercetin was evaluated for its antimicrobial potential against clinical isolates of IBD patients (HM95, HM233, HM251, HM615). Cytotoxicity was determined against human colorectal adenocarcinoma cells (Caco2, COLO.205, HT.29), whereas, cytocompatibility against normal rat intestinal epithelial (IEC-6). Results: It showed an MIC value of 5 mg/mL and MBC value of 10 mg/Ml against all the four bacterial isolates. A dose dependent response was observed against the cell lines. Conclusion: Antibacterial activity of Quercetin was found against the bacterial isolates from CD and UC patients used in the study. Cytotoxity was observed against colorectal cancer cells with minimal effect on normal cells. However, further investigations are required to understand its precise mechanism.