Adenoviruses cause a variety of diseases that range from mild to fatal in vulnerable patients. Its evolution occurs as a process of selection pressure; for example, genetic recombination generates intermediate strains that can be more infectious or pathogenic than parental strains. This study sought to determine the diversity of circulating adenoviruses in Paraguayan children less than 5 years of age hospitalized with acute lower respiratory infection, by using molecular biology and bioinformatics tools, though amplification of penton, hexon and fiber genes in 26 samples of nasopharyngeal aspirates. It was demonstrated the circulation of three species: B (4/26), C (21/26), and D (1/26), as well as recombination events corresponding to the HAdV-D isolate, with at least three different genotypes (D49, D9 y D15). The HAdV-D are associated with gastrointestinal or ocular diseases, and less commonly with respiratory infections. Recently, however, it has been reported changes in behavior of these viruses due to recombination, allowing them to expand their host cell repertoire. These data extend the knowledge about the genetic diversity of HAdV in Paraguay and strongly support the importance of genomic analysis using bioinformatics tools in epidemiological surveillance of emerging recombinant strains of HAdV.