Background <p>CD103⁺ tissue-resident memory T cells was detected in various solid malignancies, like colorectal cancer (CRC), and associated with improved survival. However, clinical significance of CD103⁺ cells in specific intratumor compartment remains unclear.</p> Methods <p>The abundance and distribution of CD103⁺ cells were assessed using immunohistochemistry and quantified separately for 3 compartments, including intraepithelial compartments at center of tumor (CT-IEL), stromal compartments at center of tumor (CT-ST) and invasive margin (IM) in a cohort of 224 CRC patients under radical surgery and correlated with outcome. Findings in each compartment were then validated in an external validation cohort comprising 294 CRC patients.</p> Results <p>Elevated density of CD103⁺ cells infiltration in the CT-IEL, CT-ST or IM compartment was correlated with favorable survival in both the initial discovery cohort and subsequent validation cohort. Notably, abundant CD103⁺ cells located in the CT-IEL compartment was remained an independent prognostic indicator for CRC patients by multivariant analysis. Characterization study showed that intraepithelial CD103⁺ cells were predominantly single positive CD8 T cells. Conversely, CD103⁺ cells exhibited a heterogeneous population comprising CD103⁺CD8⁺ cells, CD103⁺CD4⁺ cells, and nonconventional CD103⁺CD4⁺CD8⁺ cells in the CT-ST and IM compartments. Finally, a CD103 score was generated comprising abundance of CD103⁺ cells in the 3 compartments. This score had the highest relative contribution to the risk of all clinical parameters for prognosis in both cohorts.</p> Conclusion <p>This study supported a phenotypic heterogeneity of CD103⁺ cells in CRC, and provided a reliable estimate of the risk of death and recurrence in CRC patients based on combined analysis of CD103⁺ cells within 3 intratumor compartments.</p>