Aim:The purpose of this study was to assess the association with automated US measurements of carotid artery intima-media thickness (cIMT) with anthropometric, laboratory data and ultrasonographic measurements of fat, in order to identify potential markers that could be used to prevent the development and progression of cardiovascular pathology in adolescents. Method: Forty-five patients aged 10 to 17 years were enrolled in this study. Blood samples and anthropometric measurements were obtained from all subjects. All patients underwent an ultrasonic assessment of subcutaneous tissue, pre-peritoneal fat, and intra-abdominal fat. All patients received an US assessment of the common carotid artery intima-media thickness. Results: There was a positive association of minimum beds of pre-peritoneal fat, on both sides, with cIMT. Additionally, cIMT on the right side was positively associated with HOMA-IR. In our multivariate analysis, HOMA-IR remained independently associated with cIMT (left) and measurement of the minimum bed of pre-peritoneal fat was associated with right cIMT. There was no association of cIMT with sex, BMI z-score, demographic variables or laboratory findings. Conclusion: Pre-peritoneal fat and HOMA-IR are associated with automated ultrasound measurements of both carotid intima-media thickness. Carotid intima-media thickness was not associated with any other demographic variables nor with other laboratory findings when assessed with our automated US method.