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Abstract Objective Severe growth hormone deficiency (GHD) leads to several metabolic effects in the body ranging from abnormal body composition to biochemical disturbances. However, less is known regarding these parameters in short children with GH peak levels in the lower normal range during provocation tests. Our aim was to study the metabolic profile of this group and compare it with that of healthy children of normal height. Design Thirty-five pre-pubertal short children (<− 2.5 SDS) aged between 7 and 10 years, with peak levels of GH between 7 and 14 μg/L in an arginine insulin tolerance test (AITT), were compared with twelve age- and sex-matched children of normal height. The metabolic profile of the subjects was analysed by blood samples, DEXA, frequently sampled intravenous glucose tolerance test, microdialysis and stable isotope examinations of rates of glucose production and lipolysis. Results There were no overall significant metabolic differences between the groups. However, in the subgroup analysis, the short children with GH peaks < 10 μg/L had significantly lower fasting insulin levels which also correlated to other metabolic parameters. Conclusion The short pre-pubertal children with GH peak levels between 7 and 14 μg/L did not differ significantly from healthy children of normal height but subpopulations within this group show significant metabolic differences.