OBJECTIVES: Some patients with lower rectal cancer develop "skip metastasis," in which lymph node metastasis occurs in the lateral but not the mesenteric lymph nodes. However, the prognostic impact of skip metastasis is unclear. This study aimed to determine the long-term prognosis of skip metastasis in lower rectal cancer. METHODS: This retrospective study included patients with stage I-III lower rectal cancer who underwent total mesorectal excision and lateral lymph node dissection at our institution between 2000 and 2019. We investigated the association of lymph node metastasis with relapse-free and overall survival. Multivariate analyses were performed using Cox proportional hazards regression models. RESULTS: Of a total of 371 patients, 183 (49%) were negative for lymph node metastasis, 115 (31%) were positive for mesenteric lymph nodes only, 18 (5%) were positive for lateral lymph nodes only (skip metastasis), and 55 (15%) were positive for both mesenteric and lateral lymph nodes; the 5-year relapse-free survival rates were respectively 79.9%, 60.0%, 68.3%, and 32.7%, and 5-year overall survival rates were 96.6%, 90.0%, 85.6%, and 57.3%. Multivariable analysis revealed significant differences in relapse-free and overall survival between those positive for both mesenteric and lateral lymph nodes and those positive for lateral lymph nodes only (relapse-free survival, hazard ratio 2.30, p=0.048; overall survival, hazard ratio 3.50, p=0.030). CONCLUSIONS: In patients with lower rectal cancer who underwent total mesorectal excision and lateral lymph node dissection, those with skip metastasis had better relapse-free and overall survival than those with both mesenteric and lateral lymph node metastases.