Background Obesity, as measured by body mass index, is widely recognized as a risk factor for the development of cardiovascular disease. However, the role of body composition components such as fat and lean mass is not well studied. Methods and Results A total of 3129 patients who underwent computed tomography scans for quantification of coronary artery calcification and had bioelectrical impedance analysis of body composition (fat mass and fat‐free mass) during exam 5 of MESA (Multi‐Ethnic Study of Atherosclerosis) were included in this cross‐sectional analysis. Multivariable adjusted linear regression analysis was performed to assess the relationship between both fat mass and fat‐free mass to prevalent coronary artery calcification, a marker of subclinical coronary artery disease quantified by both the coronary artery calcification (CAC) Agatston score and the spatially weighted calcium score. CAC and spatially weighted calcium score were natural log–transformed for analysis as continuous variables. Fat‐free mass, but not fat mass, was independently associated with CAC. There was a 7.6% prevalence risk difference for CAC>0 per 10 kg. Fat‐free mass was also significantly associated with natural log of CAC (coefficient=0.272, P <0.001). Both fat‐free mass and fat mass were positively associated with natural log of spatially weighted calcium score, with risk difference coefficients of 0.729 and 0.359, respectively ( P <0.001). Conclusions In this cross‐sectional study, higher lean mass by bioelectrical impedance analysis and, to a lesser extent, higher fat mass by bioelectrical impedance analysis were significantly associated with higher coronary calcium, a marker of subclinical cardiovascular disease. Further exploration of the relationship between components of body composition and the development of cardiovascular disease is warranted.