Summary Background Infants born small‐for‐gestational‐age (SGA) who develop post‐natal weight catch‐up are at risk for insulin resistance, central adiposity and cardiovascular disease in later life, even in the absence of overweight. Objective In young (age 3–6 years) non‐obese SGA children, we assessed arterial health (as judged by intima‐media thickness IMT) and abdominal fat distribution (subcutaneous, visceral, preperitoneal and hepatic components by magnetic resonance imaging MRI and/or ultrasound US) besides a selection of endocrine markers. Methods Comparisons of measures in SGA (n = 27) vs. appropriate‐for‐GA (AGA) children (n = 19) of similar height, weight and body mass index. Longitudinal outcomes (age 3–6 years) were carotid IMT (cIMT); fasting glucose, circulating insulin, IGF‐I and high‐molecular‐weight (HMW) adiponectin; abdominal fat partitioning by US. Cross‐sectional outcomes (age 6 years) were aortic IMT (aIMT) and abdominal fat partitioning by MRI. Results At 3 and 6 years, cIMT and IGF‐I results were higher and HMW adiponectin lower in SGA than AGA children; at 6 years, SGA subjects had also a thicker aIMT and more pre‐peritoneal and hepatic fat, and were less insulin sensitive (all P values between <0.05 and <0.0001). cIMT correlated positively with pre‐peritoneal fat, particularly at 6 years. Post‐SGA status and weight gain in early childhood (between 3 and 6 years) were independent predictors of cIMT at 6 years, explaining 48 % of its variance. Conclusion SGA children aged 3–6 years were found to have a thicker intima‐ media and more pre‐peritoneal and hepatic fat than AGA children of comparable size.