Obesity is the major determinant of metabolic syndrome. Being born small for gestational age (SGA) may be co-responsible. We aimed at evaluating the association between 1. obesity and 2. being born SGA and the presence of endocrine-metabolic abnormalities in prepubertal Slovak children. The study included 98 children, aged 3-10.9 years: 36 AGA-born obese children (OB), 31 SGA-born children (SGA) and 31 appropriate for gestational age born non-obese children (AGA). Fasting serum levels of glucose, total cholesterol, LDL, HDL, triglycerides, fT4, TSH, cortisol and insulin were determined. HOMA-IR was calculated. Personal data about birth weight and length and family history were collected. Actual anthropometric measurement was done. In every group, high prevalence of positive family history of metabolic disorder was found. In comparison with AGA children, OB children were taller (p<0.01) with higher body mass index (BMI) (p<0.001), and had increased insulin levels and homeostasis model assessment for insulin resistance (HOMA-IR) (p<0.001), decreased high-density lipoprotein (HDL) (p<0.001), and a trend to higher cortisol levels (p=0.069) was noted. SGA-born children were shorter (p<0.001), with BMI comparable to the AGA group. They had higher glucose levels (p<0.001), a trend to decreased HDL levels (p=0.085) and increased fT4 levels (p<0.001). A three-fold higher occurrence of metabolic abnormalities was present in obese children and twice more metabolic abnormalities were present in SGA-born children in comparison with AGA-born children. SGA-born children are more prone to developing endocrine-metabolic abnormalities than non-obese children born AGA, but they are at less risk than obese AGA-born children. We should provide specialized care for obese children already in prepubertal age and pay attention to SGA-born children.