Background: Colorectal cancer (CRC) is divided into 2 groups based on genomic differences: chromosomal instability (80%), and microsatellite instability (MSI) (20%). MSI CRC is associated with a favorable prognosis independent of classic clinical prognostic factors. MSI CRC has been characterized by an intense immune infiltration which was assumed to be related to a high density of mutations creating numerous neoantigens. We compared the nature of inflammation in MSS and MSI CRC specimens to identify biomarkers which could guide therapeutic interventions. Methods: Pairs of CRC and normal tissues were enzymatically dissociated to isolate leukocytes by density gradient and their phenotypic characterization was done via multi-parameter flow cytometry (MFC). Immune infiltration was scored using immunohistochemistry (IHC) and in situ molecular analysis was performed via laser capture microdissection (LCM) and TaqMan quantitative RT-PCR. Results: IHC analysis of immune infiltrates in 15 CRC specimens delineated 3 distinct areas denominated intraepithelial lymphocytes (TIL), tumor stroma (TS) and invasive margin (IM). Scoring of CD3⁺, CD4⁺ and CD8⁺ cells demonstrated that MSI specimens (n=8) were characterized by a higher infiltration of all three populations compared to MSS samples (n=7). Molecular analysis of the TIL (3 MSI versus 3 MSS) indicated that the tumor microenvironment of MSI CRC was characterized by a high expression of IFNg and genes associated with cytotoxic T cells (CTL) including CD8A, TBX21, PERF, GZM. Strikingly, MSI samples had a greater expression of IFN-g-driven immune checkpoints such as PD-1, PD-L1, IDO-1 and INOS suggesting that the high density of infiltrating CTL and IFNg stimulate mechanisms of adaptive immune resistance in MSI tumors. MFC analysis of TIL performed on fresh tumors confirmed the higher presence of IFNg-producing PD1^hi CD8⁺CTL in MSI samples (n=8). Conclusions: The genetic origin of CRC dictates the nature and intensity of inflammation. A strong IFNg -driven inflammatory response in MSI CRC patients triggered the expression of PD-L1 and IDO-1 which could be targeted to enhance clinical benefit and be predictive of response to immune checkpoint inhibitors.