The diversity and succession of epidemiologically significant enteroviruses (EV) lead to constant changes in the clinical presentation and morbidity levels. The aim of the study is to investigate cases of EV infection in hospitalized children during the resurgence of the epidemic process following the COVID-19 pandemic. We collected clinical samples from 156 patients with EV infection across a range of ages. Virus genotyping was performed using the Sanger sequencing of the 5’UTR-VP2 and VP1 genome fragments. Sixteen types of enteroviruses were identified, with one additional case identified only to the species level (EV-C). The dominant EV type was Coxsackie CV-A6, with a share of 80.6% (95% CI: 66.7–95.5) in 2021 and 36.1% (95% CI: 27.5–44.6) in 2022. Most commonly, CV-A6 caused skin lesions (exanthema or HFMD) and respiratory manifestations. In 2022, the proportion of CV-A10 cases increased considerably to 27.0% (95% CI: 19.2–34.9) compared with 6.4% (95% CI: 0–15.1) in 2021. The most common clinical manifestation of CV-A10 was herpangina. The most severe EV infection cases were associated with ECHO 6 — four out of 11 patients were diagnosed with meningitis, while the remaining patients exhibited neurological symptoms (meningism, intense headache, vomiting) accompanied by fever. We observed a large number of EV cases accompanied by the presence of other infectious agents in biological samples, which may result from immune suppression during EV infection development. The most common of these agents was human herpesvirus 6 (HHV-6). The nucleotide sequences of the characterized enteroviruses have been deposited in the NCBI database to enable subsequent epidemiological analysis of enterovirus circulation in the Russian Federation.