In infants, urinary tract infections (UTIs) are quite common and primarily caused by bacterial pathogens. However, little research has been conducted regarding the relationship between uropathogenic bacteria, virulent genes, and uropathogenic viruses that might induce UTIs in infants. In this study, we evaluated infants with UTIs to determine the influence of bacterial virulent genes and type of viral infections on clinical aspects. First, we detected 44 cases of bacterial UTI from 600 suspected cases in infants and children. We detected E. coli urovirulence genes (kps, usp, pap, ireA, and cnf), two enteropathogenic E. coli genes (bfpA, and eae) and four S. aureus and S. epidermidis genes (mecA, pvl, bbp, and icaA) in urine samples from infant UTI cases. We also simultaneously detected hematuria-related adenovirus type 11, 21, and BK virus (BKV) in urine samples by PCR. As a result, E. coli was the most prevalent bacteria and in Dimercaptosuccinic acid (DMSA)-positive UTI cases, the uropathogenic E. coli virulence factor pap was significantly high. We found that BKV detection was significantly higher in DMSA-positive UTI infants (89%) compared with 50% of non-UTI (no bacteria detected) cases. These results are indicative of combined multiple bacterial and viral infections and show severe infant pyelonephritis.