The purpose of the study was to compare the health-related fitness levels between two clusters of Kendriya Vidyalaya (KV) high schools, viz. Hassan and Mangalore clusters. sports activities and physical education are almost equal in all KV schools, but there may be differences related to demographic, food habits, culture, etc. There are also the probable significant differences in the health-related fitness levels of students in relation to their places of residences. The health-related fitness variables selected for study were flexibility, muscular strength, muscular endurance. cardiovascular endurance and body composition (BMI). To achieve the purpose of the study, data was collected from two hundred students, one hundred from each cluster. The age of the subjects ranged from 14 to 18 years. ‘Sit and-reach’ test, ‘twokilometre walk-and-run’ test, ‘partial curl-up’ test, push up and BMI measurements were taken as variables to test fitness components. To know the mean difference between groups, t-test was computed. The results revealed that there is a significant difference in the health-related fitness levels. The Hassan students were superior in height, flexibility whereas Mangalore students were superior in muscular strength, muscular endurance, cardio-vascular endurance, and BMI. It was concluded that the food habits and lifestyle of two different cities could be the major cause of the physical fitness difference between the students in different clusters.