Background/Aim: This study aimed to analyze the correlation between microsatellite instability (MSI) and inflammatory markers during neoadjuvant CRT in rectal cancer and its influence on prognosis. Patients and Methods: A total of 549 patients with locally advanced rectal cancer underwent neoadjuvant CRT. Complete blood counts before CRT, and 4-8 weeks after CRT were used to measure neutrophil-to-lymphocyte ratio (NLR) and platelet-tolymphocyte ratio (PLR). Results: MSI was significantly associated with elevated NLR and PLR after CRT as well as with a change in NLR and PLR during CRT. Neither inflammatory markers nor MSI significantly related to survival. However, in patients with MSI, an increase in NLR and PLR before CRT was significantly correlated with poor overall survival and disease-free survival. Conclusion: There is correlation between inflammatory markers and MSI during CRT and it influences prognosis. Therefore, inflammatory markers might have a role in assessing the microenvironment related to MSI and the immunologic response in rectal cancer. Chemotherapy and radiotherapy have the potential to reprogram the tumor microenvironment and induce immunostimulatory effects, possibly by encouraging tumor antigen-specific immune response (1). In rectal cancer, neoadjuvant chemoradiotherapy (CRT) has been widely used in patients with locally advanced rectal cancer. We have previously reported that inflammatory markers including a neutrophil-to-lymphocyte ratio (NLR) and platelet-tolymphocyte ratio (PLR) can be used as a predictive marker of treatment response after neoajduvant CRT (2). In previous studies, inflammatory markers have been shown to have a direct correlation with the intra-tumoral levels of granulocyte myeloid-derived suppressor cells and regulatory T cells (3, 4), which can suppress anti-tumor immune reaction (1). Furthermore, the inflammatory markers have been recently found to predict the response of immunotherapy (5, 6). Microsatellite instability (MSI) is one of the well-known immunologic markers in colorectal cancer, which tends to induce hyper-mutation and exhibit peri-tumoral immune cell infiltration/activation closely related to the change in tumor 2119 This article is freely accessible online.