Background: Febrile seizures (FS) are common in young children. Viral infections that result in high fever are frequent etiologic agents that lead to febrile seizures. Human Herpesvirus 6 (HHV6), Influenza virus, adenovirus, and enterovirus have been named as the most common viruses causing high fevers in young children. Although bacterial infections have rarely been found as causative agents, many children with febrile seizures are treated with empiric antibiotics. Objectives: To determine the epidemiology of the viral (HHV6, Adenovirus, HSV1, Enterovirus) and bacterial infection in children presenting with febrile seizures. Methods: In a descriptive study, data was collected from 93 children, 3 months to 5 years of age, hospitalized with febrile seizures between September 2016 and April 2017. Relevant information was documented on a previously designed questionnaire. Blood samples were collected for culture, Serum 16S rRNA for bacteria, and PCR assay for 4 viruses (HHV6, adenovirus, enterovirus and HSV), in addition to routine investigations. Results: Of the 93 patients, serum PCR results were negative for 73 patients (78.49%) and 15 (16.13%) were positive for viruses (11 for HHV6 and 4 for Adenovirus). Serum 16S rRNA for bacteria was detected in 5 cases and blood culture was positive in 4 cases. Conclusions: Findings of this study indicate a significant prevalence of viruses and a very low rate of bacterial infection in children with febrile seizures, thus, negating the use of empirical antibiotic therapy.