The study aimed to investigate the relationship between heart-carotid pulse transit time and carotid intima-media thickness (CIMT) in hypertensive patients, and whether including the pre-ejection period (PEP) in heart-carotid pulse transit time would affect this correlation. A total of 62 hypertensive patients were included in this study. They were divided into the normal CIMT group (n=33, CIMT⩽0.8 mm) and the thickened CIMT group (n=29, CIMT>0.8 mm). The noninvasive ultrasound method was used to measure CIMT, electrocardiogram R-wave-based heart-carotid pulse transit time (rcPTT) and PEP. Aortic valve-carotid artery pulse transit time (acPTT) was calculated by subtracting PEP from rcPTT. Simple linear analysis showed that CIMT was negatively associated with rcPTT and acPTT (r=-0.57, P<0.0001; r=-0.41, P=0.016) in the normal CIMT group as well as in the thickened CIMT group (r=-0.50, P=0.0053; r=-0.59, P=0.001). These relationships were eliminated in the normal CIMT group after adjusting for age, gender, smoking behaviour, systolic blood pressure, diastolic blood pressure and cholesterol levels. However, rcPTT and acPTT still showed significant correlations with CIMT in the thickened CIMT group. In conclusion, rcPTT and acPTT were associated with CIMT, independent of well-known clinical confounders in thickened CIMT hypertensive patients. Therefore, rcPTT and acPTT might be useful markers for atherosclerosis evaluation.