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Follow up studies of children with congenital heart disease, premature birth, small for gestational age syndrome and attention deficit hyperactivity disorder show significantly reduced 24-hours heart rate variability (HRV) that indicate autonomic dysfunction. The underlying pathophysiological process is of high clinical importance if autonomic dysfunction in these children is related to neurocognitive impairment, an enhanced cardiovascular risk, and a higher risk of short stature. Elevated norepinephrine levels, reduced HRV and MRI imaging indicate brain injury very early in life. We introduce the term autonomic imprinting to explain how early life stress have a lifelong imprinting effect on the autonomic nervous system. Many efforts are done for a careful management of infants in pediatric intensive care units. However, early life stress cannot be prevented if sympathetic activation is part of the underlying disease most of all due to congestive heart failure. We could demonstrate that beside a careful management, pharmacotherapy has a high impact on autonomic dysfunction in children with heart failure, attention deficit disorder and short stature. Moreover, online HRV monitoring is a complete noninvasive tool to monitor early life stress if it uses the data from routine heart rate monitoring. HRV online monitoring on the pediatric intensive care unit and Holter ECG monitoring in a daily life setting are clinical routine in our department for each pharmacotherapy affecting the autonomic nervous system. In the same time as monitoring of early life stress becomes clinically routine, the situation of children will improve if we realize which interventions increase early life stress or improve its detrimental damages in longtime follow up.