Background: Zinc (Zn) deficiency has been linked with etiology for wide range of gastrointestinal diseases. Although low serum Zn has been associated with diarrhea and growth retardation, however the underlying mechanism of Zn deficiency aggravating the diarrheal manifestation remains elusive. Here, we have studied the physiological cascade elicited during Zn deficiency in both colonic cell lines and murine model leading to altered intestinal barrier function and ion transport. Methods and materials: T84 were grown onto transwell inserts in Zn deficient conditions for measurements of transepithelial electrical resistance (TER) and short-circuit current (Isc). Adult BALB/c mice fed with Zn deficient diet for 14 days and were intraperitoneally challenged with virulent S.flexneri 2a for following assessments of electrophysiological properties of the colonized colon in ussing chamber. Colonization evaluation from feces and colon homogenate were further analyzed for bacterial translocation assay. Results: Zn deficient cells infected with Shigella flexneri 2a showed significant increase in transmigration of the pathogens (6.58 ± 0.13 vs 7.98 ± 0.23 log10 CFU/ml) for 6 h post infection along with poor formation of transepithelial resistance (1014 + 165 Ωcm2 vs 3663 + 293 Ωcm2). Ultrastructure of T84 cells grown in Zn deficient medium showed widened TJ complex and due to few membrane fusion proteins showing distorted TJ morphology and shorthened microvilli. Immunoblotting analysis further showed increased expression of Claudin-2 leaky tight junction protein in Zn deficient cells by modulating ERK dependent pathways. Following studies with Ussing chambers further demonstrated increase in Ca2+ dependent electrogenic Cl− secretion in Zn deficient cells. In vivo studies showed Zn deficient condition in mice increased bacterial translocation, colonization, bacterial shedding and pronounced disruption in intestinal permeability. Conclusion: Our results suggest that in T84 cells and murine of Shigellosis, Zn deficiency causes (1) pronounced barrier dysfunction and (2) altered Cl− secretion leading to heightened diarrheal pathogenesis thus linking micronutrient deficiency with bacterial infection and inflammation.