Inappropriate sinus tachycardia (IST) is a common disease of the autonomic nervous system in children and adults. Diagnosis and treatment of IST in adolescents is not well defined. In this retrospective study, we tested our hypothesis regarding autonomic dysfunction in childhood by analyzing 24-h heart rate variability (HRV) in 479 children, with a mean age of 13.7 ± 2.1 years, who were referred to the outpatient clinic in the Pediatrics Department within the last 15 years. Seventy-four adolescents with a mean 24-h heart rate ≥ 95 bpm (our cut-off for an IST based upon 66 healthy controls) were deemed to have IST. We found the risk of IST to be high in adolescents with attention deficit disorder (OR = 3.5,p<0.001), pre-hypertension (OR = 2.5, p = 0.043) and hypertension (OR = 2.1,p = 0.02); insignificantly enhanced in children with short stature (OR = 1.9,p = 0.19), surgically-treated congenital heart disease (OR = 1.4,p = 0.51) and obesity without hypertension (OR = 1.4;p = 0.25); and negligible in adolescents with anorexia nervosa (OR = 0.3, p = 0.26) and constitutional thinness (OR = 0.9,p = 0.89). IST was associated with a significant decrease in global HRV and elevated blood pressures, indicating an enhanced cardiovascular risk. Methylphenidate did not increase 24-h heart rates, whereas omega-3 fatty acid supplementation significantly decreased elevated heart rates and increased HRV in adolescents with IST. In this retrospective analysis, 15.4% of adolescents suffered from IST with a 24-h heart rate ≥ 95 bpm, predominately due to attention deficit disorder and hypertension.