Introduction. Some of the gut-brain-adipose tissue peptides play an important role in growth hormone (GH) secretion and in the regulation of food intake. Based on the molecular mimicry hypothesis, intestinal microbe-derived antigens may trigger the production of autoantibodies cross-reacting with many regulatory peptides and modify their actions. The aim of the study was to assess ghrelin, leptin, orexinA and alpha-melanocyte-stimulating-hormone (αMSH) serum concentrations and autoantibodies against the aforementioned peptides levels in children with idiopathic short stature (ISS) and with GH deficiency (GHD) in relation to Helicobacter pylori (H.pylori) and Candida albicans (C.albicans) infections. Material and methods. The study group comprised 89 short children (aged 10.24±3.52 years): 64 with ISS and 25 with GHD and 36 normal height children (Controls) (aged 11.41±2.72 years). In each child, the concentration of ghrelin, leptin, orexinA and αMSH, the level of IgG autoantibodies against mentioned peptides as well as against H.pylori were assessed in serum, while presence of C.albicans – in stool samples. The control group was selected in such a manner that the prevalence of H.pylori and C.albicans was similar to the study group. Results. The levels of IgG antibodies against ghrelin and leptin were significantly higher in ISS than in Controls. In GHD children, the ghrelin concentrations were significantly higher than in Controls. In ISS children the leptin concentrations (as well as body mass index) were significantly lower than in GHD and in Controls. We did not find any differences among groups as regards orexinA and αMSH concentrations. Conclusions. The higher levels of autoantibodies against ghrelin and leptin in children with ISS may be connected with worse growth and lower body mass in these children through the modification of ghrelin and leptin activity. It is possible that these autoantibodies are formed in molecular mimicry mechanism between H.pylori and C.albicans and the aforementioned neuropeptides. However, further studies are necessary.