Studies have suggested that being slightly overweight but fit is better for cardiovascular health than being somewhat leaner but unfit. Here, we sought to determine the contribution of cardiorespiratory fitness (CRF), relative to the presence of risk factors, to common carotid intima-media thickness (CIMT), a measurement of atherosclerosis and cardiovascular disease risk. Data were analysed from a cohort of 7300 German employed individuals aged 46 (±7)years who participated in a preventive health check-up at a specialized prevention centre. In addition to traditional cardiovascular disease risk factor assessment, participants performed an exercise test with spirometry to exhaustion, and common CIMT was measured. Individuals were defined as being fit or unfit based on the median age- and sex-specific relative maximum oxygen consumption. In a multivariable analysis, there was a strong inverse association between CRF and common CIMT. Individuals who were considered fit and did not have any cardiovascular disease risk factors had the lowest common CIMT values (reference group). Those who were unfit and had an increased risk factor level always had the highest common CIMT values. Good CRF partly compensated for the increased common CIMT due to a risk factor. However, unfit individuals without increased risk factor levels had a common CIMT that was not significantly different from that of the reference group, whereas fit individuals who smoked, had a high body mass index, a low HDL cholesterol concentration or a high systolic blood pressure had an increase in common CIMT. Cardiorespiratory fitness is a major determinant of common CIMT. Improved CRF does slightly, but not completely, abolish the adverse consequences of cardiovascular disease risk factors on common CIMT.