The present prospective observational study was conducted to examine the differences in longitudinal associations of the conventional risk factors for cardiovascular disease (CVD) with arterial stiffness and with abnormal pressure wave reflection using repeated measurement data. In 4016 healthy middle-aged (43 ± 9 years) Japanese men without CVD at baseline, the conventional risk factors for CVD, brachial-ankle pulse wave velocity (brachial-ankle PWV) and radial augmentation index (rAI) were measured annually over a 9-year period. Mixed-model linear regression analysis demonstrated a significant independent positive longitudinal association of the mean blood pressure with both the brachial-ankle PWV (estimate = 5.51, standard error = 0.30, P < 0.01) and the rAI (estimate = 0.19, standard error = 0.02, P < 0.01). On the other hand, the serum levels of glycohemoglobin, low-density lipoprotein cholesterol and triglycerides showed longitudinal associations only with the brachial-ankle PWV and not the rAI. In addition, while the radial AI was found to show a significant longitudinal association with the brachial-ankle PWV, the inverse association was not significant. In conclusion, the conventional risk factors for CVD showed heterogeneous longitudinal associations with arterial stiffness and/or abnormal pressure wave reflection. Elevated blood pressure showed independent longitudinal associations with both arterial stiffness (macrovascular damage) and abnormal pressure wave reflection, suggesting that BP is also longitudinally associated, at least in part, with microvascular damage. On the other hand, abnormal glucose metabolism and dyslipidemia showed independent longitudinal associations with only arterial stiffness (macrovascular damage).