Background: Most data on mortality and prognostic factors of universal healthcare waiting lists come from North America, Australasia, and Europe, with little information from South America. We aimed to determine the relationship between medical center-specific waiting time and waiting list mortality in Chile. Method: Using data from all new patients listed in medical specialist waitlists for non-prioritized health problems from 2008 to 2015 in three geographically distant regions of Chile, we constructed hierarchical multivariate survival models to predict mortality risk at two years after registration for each medical center. Kendall rank correlation analysis was used to measure the association between medical center-specific mortality hazard ratio and waiting times. Result: There were 987,497 patients waiting for care at 77 medical centers, including 33,546 (3.40%) who died within two years after registration. Male gender (hazard ratio [HR] = 1.17, 95% confidence interval [CI] 1.1-1.24), older age (HR = 2.88, 95% CI 2.72-3.05), urban residence (HR = 1.19, 95% CI 1.09-1.31), tertiary care (HR = 2.2, 95% CI 2.14-2.26), oncology (HR = 3.57, 95% CI 3.4-3.76), and hematology (HR = 1.6, 95% CI 1.49-1.73) were associated with higher risk of mortality at each medical center with large region-to-region variations. There was a statistically significant association between waiting time variability and death (Z = 2.16, P = 0.0308). Conclusion: Patient wait time for non-prioritized health conditions was associated with increased mortality in Chilean hospitals.