BACKGROUND Endurance running performance is dependent upon hematological, physiological, anthropometrical, diet, genetic, and training characteristics. Increased oxygen transport and efficiency of tissue in extracting oxygen are the major determinants to competitions that require endurance. Thus, altitude training is often employed to increase blood oxygen-carrying capacity to improve sea-level endurance performance. This study aimed to compare hematological parameters of endurance runners' training at different clubs with different altitudes (Guna Athletics Sport Club at Guna (3100 meter above sea level) and Ethiopian Youth Sport Academy at Addis Ababa (2400 meter above sea level)). METHODS A comparative cross-sectional study was conducted at GASC and EYSA. Data were collected from a total of 102 eligible study subjects (26 runners and 25 controls at Guna and 26 runners and 25 controls at Addis Ababa) from May to October 2019. About 3 ml of the venous blood was drawn from the antecubital vein by aseptic procedure and analyzed using a hematology analyzer (DIRUI BCC-3000B, China). One-way ANOVA and independent-sample t-tests were used to compare means. RESULTS Male runners in Guna had significantly higher hemoglobin (Hgb), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and white blood cell (WBC) count than male runners in Addis Ababa. Besides, female runners in Guna had significantly higher MCH and MCHC than female runners in Addis Ababa. However, there were no significant differences between Guna and Addis Ababa runners in red blood cell (RBC) count, Hct, MCV, and platelet count in both sexes, while Hgb and WBC count in females. CONCLUSIONS Decisively, Guna Athletics Sport Club endurance runners had significantly higher hematological parameters than Ethiopian Youth Sport Academy endurance runners. This provides invaluable information for coaches and sport physicians to monitor the hematological profile and the health status of an athlete living and training at different altitudes.