Background To report quality control methods and baseline reproducibility data of the ultrasound measurements of carotid artery intima-media thickness in the project of Establishment of an Integrated System for Coronary Heart Disease Prevention and Treatment. Methods Standard ultrasound scanning and measuring protocols were established by the study group. All sonographers and readers were trained by the carotid ultrasound core lab and all digital ultrasound images were centrally read. Ten subjects were scanned twice (with 1 week interval) by 2 sonographers independently and images were read by a single reader to evaluate the sonographer variability. Twenty subjects’ images were read twice (with 1 week interval) by a single reader to assess the reader variability and the reproducibility of IMT measured at different carotid segments. Results The intraclass correlation (ICC) of intra- and inter-sonographer and intrareader for mean IMT measurements was 0.99, 0.98 and 0.97 respectively; while for max IMT, it was 0.97, 0.99 and 0.95 respectively. Among different carotid segments and sites, ICC for mean IMT measurements of common carotid (CCA), carotid artery bulb (Bulb), internal carotid artery (ICA), overall near wall and overall far wall was 0.97, 0.99, 0.89, 0.93 and 0.98 respectively. Conclusion The reproducibility of IMT measurements according to our protocol is acceptable, although better reproducibility is found when measuring the mean IMT than max IMT, CCA and Bulb IMT than ICA IMT, and far wall IMT than near wall IMT.