Abstract Background To examine whether lower insulin sensitivity as determined by homeostatic model assessment (HOMA-%S) was associated with increased left ventricular mass (LVM) and presence of LV diastolic dysfunction at long-term follow-up, independently of body mass index (BMI), in middle-aged, otherwise healthy males. Methods Prospective population-based cohort study with a median (IQR) follow-up time of 28 (27–28) years, in which traditional cardiovascular risk factors, including HOMA-%S and BMI, were assessed at baseline, and echocardiographic determination of LVM and LV diastolic function was performed at follow-up. Associations between risk factors and echocardiographic variables were tested using multivariable linear and binary logistic regression. Results The study population comprised 247 men with a median (IQR) age of 47 (47–48) years. Mean (SD) BMI was 25.1 +/− 3.0 kg/m2, and median (IQR) HOMA-%S was 113.0 (68.3–284.6). Subjects with low insulin sensitivity (lowest HOMA-%S quartile (Q1)) had significantly greater BMI, fasting plasma insulin, and higher fasting blood glucose (FBG) (p