Introduction and objective: Short stature is a common paediatric problem. Some children with short stature present growth hormone (GH) deficiency (GHD), whereas others have no hormonal disturbances (idiopathic short stature, ISS). Distinguishing between these two conditions is the task of the paediatric endocrinology centres. The aim of this study was to compare the clinical picture and hormonal tests results in patients with short stature caused by GHD and ISS. Materials and methods: The study included 100 short stature children. In all the children, medical history was obtained and a physical examination was performed. Next, bone age, insulin-like growth factor type 1 (IGF-1) levels, and GH secretion in two stimulation tests were assessed. With respect to the GH results, the children were divided into two groups: GHD (n = 38) and ISS (n = 62). Results: There were no significant differences between the groups with respect to age, sex, puberty stage, bone age, birth length and birth weight. Growth retardation was observed in both groups with a similar frequency, but in the ISS group it occurred significantly earlier. The mother’s height was lower in the ISS group. Body mass was significantly higher, but IGF-1 significantly lower in the GHD group. In both groups, the maximum GH secretion in the stimulation tests was higher after clonidine than after glucagon, which indicates that this test is more reliable. Conclusions: A similar degree of growth deficiency, growth rate deceleration and bone age delay are observed in ISS and GHD children, though ISS children are thinner and have higher IGF-1 levels. Despite some differences in clinical presentation, all short stature patients with growth rate deceleration should undergo thorough diagnostic testing along with GH stimulation tests.