Abstract Background Blood pressure variability (BPV) has been associated with development, progression and severity of cardiac and vascular organ damage and with an increased risk of cardiovascular events and mortality, independently adding to cardiovascular risk, over and above the contribution of elevated mean BP levels. We aimed to explore any correlation between differences in BPV and target organ damage indices (TOD) in hypertensive patients three years after medical treatment initiation. Methods At baseline and before medical treatment initiation, we measured 24h average SBP and DBP as well as 24h systolic BPV after 24h ambulatory blood pressure monitoring (ABPM) in newly diagnosed and never treated hypertensive patients (n=171, mean age=52+12 years, 110 males, 24h average SBP/DBP=138+10/87+9 mmHg, 24h systolic BPV=15+3) who were also subjected to arterial stiffness by carotid-femoral pulse wave velocity (PWV), left ventricular hypertrophy by left ventricular mass index (LVMI) and coronary flow reserve (CFR) estimations. All the above tests were repeated approximately three years later after treatment initiation. Results Patients were characterized as controlled (n=113, mean age=54+12 years, 62 males, 24h average SBP/DBP=118+6/71+6 mmHg) or non-controlled hyperensives (n=58, mean age=48+11 years, 48 males, 24h average SBP/DBP=133+8/83+7 mmHg) based on ABPM results three years later (controlled BP=24h average BP<130/80 mmHg). In the whole population, 24h average SBP/DBP, systolic BPV (p<0.001) and LVMI (p=0.01) were decreased while systolic BPV difference was related with LVMI difference (r=0.27, p<0.001). In controlled hypertensives, 24h average SBP/DBP, systolic BPV (p<0.001) and LVMI (p=0.02) were decreased while systolic BPV difference was related with LVMI difference (r=0.35, p<0.001). In non-controlled hypertensives, 24h average SBP (p=0.001), DBP p<0.001) and systolic BPV (p=0.04) were decreased while PWV was increased (p=0.03) and no correlations were found between systolic BPV and TOD. Correlation between BPV and LVMI Conclusions It seems that antihypertensive-induced systolic BPV improvement relate with cardiovascular risk decrease occur only in the setting of blood pressure treated within normal limits and confirmed by ABPM. Our study confirms that left ventricular mass between other TOD primarily improves due to successful antihypertensive treatment.