Turkey fattening is one of the most sensitive forms of poultry production. Problems with the digestive system are one of the most common and occur from the very beginning of production. The most common causes are those of viral etiology, often in the form of complexes, such as PEMS, which can cause significant losses on their own or as a result of secondary bacterial and parasitic infections. Causes such as astroviruses, rotaviruses, reoviruses, adenoviruses and others are among the most commonly isolated pathogens from the digestive system. The most common problems are vertical transmission, horizontal spreading and poor hygiene conditions that are difficult to control and prevent with biosecurity measures, which are often the only way to combat the previously mentioned pathogens. In this study, turkeys from 7 different flocks and different suppliers, aged 3 and 54 days, were submitted for search. After sacrifice, aggregate small intestinal tissue samples of five individuals were taken and stored at -80 ˚C until further analysis. After homogenization and centrifugation of the tissue, the supernatant was filtered and treated with nucleases, and nucleic acids were extracted from the purified virions from which the ribosomal RNA was removed. Samples were purified and used for the synthesis of complementary cDNA sequenced by the MiSeq (Ilumina) device. Using two types of programs on the Geneious platform, the raw sequences were joined into contigs, after which the sequenced viruses were classified to the family level, after which comparison and phylogenetic analysis were performed. The presence of astrovirus alone was detected in the samples in 3 of 7 flocks while rotavirus was detected in only one flock. Longitudinal monitoring of the positive flock proved the presence of astrovirus up to 14 days of age and absence after 30 days of age. Proven viruses show the greatest similarity with the virus originating from Poland. The results showed an early high prevalence of astrovirus and a relatively low prevalence of rotavirus, indicating the need to improve hygiene conditions and biosecurity measures on the farm, as well as a possible improvement in immunoprophylaxis on parent farms to reduce vertical pressure on production flocks.