Objective To determine the prevalence of astrovirus, norovirus, adenovirus in children below five years old with diarrhea by multiplex reverse transcriptase polymerase chain reaction (RT-PCR) along with rotavirus antigen detection by enzyme linked immunosorbant assay. Methods The study was conducted on children below five years old complaining of acute diarrhea. The study included stool examination by molecular method for detection of norovirus, adenovirus and astrovirus by multiplex RT-PCR. Rotavirus antigen was detected in the stool by enzyme linked immunosorbant assay. Results The study included 100 children below 5 years old with acute diarrhea. Multiplex RT-PCR was positive in 34% of the children. The most frequently detected virus was rotavirus (44%), followed by norovirus (30%), adenovirus (20%) and astrovirus (14%). The clinical symptoms were more significantly associated with viral diarrhea such as fever (P = 0.03), bloody diarrhea (P = 0.025), vomiting (P = 0.000 1) and watery diarrheas (P = 0.05). The frequency of diarrhea with viral pathogen was significantly presented in winter season (39.7%). There were significant frequencies of norovirus and adenovirus in age ranging 1–2 years old (P = 0.04, P = 0.01 respectively). Conclusions The present study spotlights on the prevalence of viral pathogens as an important etiology in diarrhea in children below five years old. Astrovirus, norovirus and adenovirus are common along with rotavirus in this group of patients. Multiplex PCR leads to improve the laboratory diagnosis of these viruses along with antigen detection method. Further longitudinal studies are required to evaluate the epidemiological data associated with these viruses and for proper management of such drastic infection.