We analyzed the relationship between 24-hour blood pressure variability and spatial distribution and extent of early carotid atherosclerosis in 208 hypertensive and 216 normotensive patients aged over 55 years. Circadian blood pressure patterns were evaluated noninvasively with a long-term blood pressure monitor. The extent of atherosclerosis was measured as the intima-to-media wall thickness (IMT) of the internal (ICA) and external carotid artery (ECA). No significant differences regarding age, sex, smoking, diabetes, cholesterol and triglycerides were found in either patient group. In both groups, a linear correlation between ICA and ECA IMT was observed. However, the slope of the regression line was clearly increased in hypertensive patients [0.563 (95% confidence interval 0.522, 0.604) vs. 0.436 (0.364, 0.509); p < 0.01]. Multivariate regression analysis revealed the strongest correlation between the IMT of the ICA and the diurnal systolic blood pressure variability; this parameter was not significantly associated with the ECA IMT. The odds ratio of having ischemic heart disease was significantly raised in patients with early atherosclerosis of the ICA but not the ECA [4.7 (2.5, 8.8); p < 0.001 vs. 1.6 (0.7, 3.6)]. Our results show that the diurnal systolic blood pressure variability is closely correlated with early carotid atherosclerosis of the ICA but not the ECA territory. The analysis of circadian blood pressure patterns is useful to explain the focal effects of blood pressure on the development of atherosclerosis.