There are studies reporting different results on whether there is an increased incidence of cardiovascular problems in autism spectrum disorder (ASD). The aim of this study was to examine carotid intima-media thickness (cIMT), an early marker of atherosclerosis in children and adolescents with ASD. This single-center case-control study was conducted in a tertiary care hospital. Eighty-five children (36 children with autism and 49 healthy controls) aged 6-18 were enrolled. After a clinical interview, Children's Global Assessment Scale (CGAS) and Autism Behavior Checklist (ABC) were filled out and laboratory measures were collected for ASD group. Anthropometric measurements (height, weight, waist and hip) of each participant were assessed. The cIMT was measured with an ultrasound probe on both sides of the neck. Age, gender, body mass index percentile and waist/hip ratio adjusted right/left common carotid arteries IMT and right/left bulb IMT were statistically significantly higher in the autism group than controls (0.45 ± 0.01 mm and 0.55 ± 0.01 mm, respectively, p < 0.001). We performed multiple linear regression analysis to determine statistically significant related factors of the cIMT in ASD. Early onset of autism symptoms were related with high carotid IMT ([beta] = -0.496, p = 0.01). These findings suggest that atherosclerosis may begin earlier in children with ASD, which is one of the most common neurodevelopmental disorders in childhood. The cIMT measurement, which is an easy and noninvasive method in the cardiovascular assessment and follow-up can be recommended for clinical use for individuals with ASD.