Background: The negative gradient between socio-economic status and prevalence of non-communicable disease in adulthood has prompted investigation of potential foundations based in childhood. The objective of the present study is to examine the influence of socio-geographical variations and socioeconomic status on health-related physical fitness in adolescents from a large population-based sample of Colombian ninth graders. Methods: During the 2014–2015 school years, we examined a cross-sectional component of the SER Study is a cross-sectional Body mass, height, muscular fitness (standing broad jump and handgrip tests) and cardiorespiratory fitness (20 m shuttle-run) were measured in n=52,204 14–16-year-olds. Area-level socioeconomic status was categorized from 1 to 6. A model was built by means of a step-by-step process and gradient maps were created to show physical fitness in the quartiles and the trend of physical fitness across disaggregated in Zonal Planning Units (in Spanish UPZ) in Bogotá, for each of the five health-related physical fitness variables. Results: Socioeconomic status was used as the only group-level variable and this had a significant effect on the models for all health-related physical fitness parameters except for handgrip. Cardiorespiratory fitness, standing broad jump, and body mass index increased 6.31, 2.69, and 1.45 times, respectively, on average with the maximum increase in socioeconomic status categories, when we compared two random individuals in each stratum. Conclusions: Our results suggest a significant association between health-related physical fitness variables and socio-geographical location in ninth grade adolescents from Bogotá, using a multilevel methodological approach.