Abstract Introduction Obesity in young adulthood is associated with various cardiovascular structural and functional changes, commonly used as markers of early subclinical cardiovascular disease. Whether these changes occur predominantly in relation to increased fat mass (FM) or are instead more closely related to simultaneous increases in underlying fat-free mass (FFM) that are known to occur in obesity, is incompletely understood. Purpose To investigate associations between both FM and FFM and a wide range of cardiac (left ventricular mass, LVM; end-diastolic volume, EDV; cardiac output, CO; stroke volume, SV), vascular (systolic blood pressure, SBP; diastolic blood pressure, DBP; mean arterial pressure, MAP; systemic vascular resistance, SVR) and autonomic (heart rate variability triangular index, HRVTI; baroreceptor reflex sensitivity, BRS) phenotypes commonly used to monitor the early evolution of subclinical CVD. Methods The study used data from extensive adipose and cardiovascular phenotyping of 408 healthy young adults (mean age 21 years) participating in a sub-study of the long-running ALSPAC birth cohort. We performed cross-sectional analysis using multiple imputation, multivariable linear regression and interaction testing to assess the association between both FM and FFM and cardiovascular phenotypes. Results Our study revealed that FFM resulted in a much greater increase in CO (difference in outcome per 1-SD difference in exposure β=0.58L/min, p<0.01, 95% CI=0.38, 0.77) than FM (β=0.20L/min, p=0.01, 95% CI=0.05, 0.36), following adjustment for both tissue types. FFM was also associated with an increase in LVM (β=19.1g, p<0.01, 95% CI=16.61, 21.58), EDV (β=22ml, p<0.01, 95% CI=18.18, 25.13) and SV (β=13ml, p<0.01, 95% CI=10.96, 15.75). FFM was also associated with improved autonomic and peripheral vascular function, including lower HR (β=-4bpm, p<0.01, 95% CI=-6.12, -1.95), higher HRVTI (β=2.1, p<0.01, 95% CI=0.72, 3.48) and lower SVR (β=-1.1, p<0.01, 95% CI=-2.12, -1.07), resulting in unchanged MAP despite elevations in CO. On the contrary, FM was not associated with LVM (β=-0.91g, p=0.35, 95% CI=-2.85, 1.02), and was associated with lower EDV (β=-4.62ml, p<0.01, 95% CI=-7.34, -1.88) and reduced autonomic function, as seen with HRVTI (β=-1.83, p<0.01, 95% CI=-3.02, -0.64) and BRS (β=-2.47, p=0.01, 95% CI=-4.27, -0.67). FM was also associated with increased HR (β=3.26bpm, p<0.01, 95% CI=1.57, 4.94) and increased SBP (β=2.14mmHg, p<0.01, 95% CI=1.01, 3.27) DBP (β=2.68mmHg, p<0.01, 95% CI=1.60, 3.77), and MAP (β=2.34mmHg, p<0.01, 95% CI=1.34, 3.34). Conclusion In young adults, changes in surrogate clinical markers of cardiac, vascular, and autonomic function commonly attributed solely to increases in fat mass should be interpreted with caution as they may be associated with underlying changes in FFM. Future work should focus on longitudinal studies of this cohort to confirm remodelling patterns based on these clinical markers.