Background. Elevated single blood pressure (BP) measurement can be associated with the development of hypertension-mediated target organ damage including left ventricular hypertrophy (LVH) and left atrial (LA) enlargement (LAE). However, long-term patterns of BP and their effects on LVH and LAE are poorly understood. We evaluated the association between the BP trajectories and the presence of LVH and LAE. Methods. We analyzed a total of 2,565 participants (1,267 males, 47.8 ± 6.7 years old) from the first biennial examination (2001-2002) of the Korean Genome and Epidemiology Study. The presence of LVH and LAE was identified by echocardiography performed at the 8th biennial examination (2015-2016). Latent mixture modeling was used to identify trajectories in mid-BP ((systolic BP + diastolic BP)/2) over time. Linear logistic regression was used for assessing BP trajectories with the outcomes. Results. We identified 4 distinct mid-BP trajectories: group 1 (lowest, 20.9%, n = 536), group 2 (36.2%, n = 928), group 3 (32.3%, n = 828), and group 4 (highest, 10.6%, n = 273). Compared with the lowest group, trajectories with elevated mid-BP had greater odds ratios having LVH and LAE by multivariable-adjusted regression models. Adjusted odd ratios for LVH were 2.033 (95% CI = 1.462–2.827,
P
<
0.001
) for group 2, 3.446 (95% CI = 2.475–4.797,
P
<
0.001
) for group 3, and 4.940 (95% CI = 3.318–7.356,
P
<
0.001
) for group 4. Adjusted odd ratios for LAE were 1.200 (95% CI = 0.814–1.769,
P
=
0.358
) for group 2, 1.599 (95% CI = 1.084–2.360,
P
=
0.018
) for group 3, and 1.944 (95% CI = 1.212–3.118,
P
=
0.006
) for group 4. Conclusions. Higher long-term mid-BP was an independent risk factor of cardiac structural changes such as LVH and LAE among middle-aged population.