Abstract Background Enteroviruses are most commonly associated with either mild or asymptomatic infections, however, the presence of silent carriers in the community has been proven to play a crucial role in the spread of diseases such as HFMD that records high incidence in Asia Pacific region. In the Philippines, limited information is available on the etiology and prevalence of enterovirus outside the Acute Flaccid Paralysis (AFP) surveillance. Methods Duplicate stool sampleswere collected from 360 healthy children. Virus isolation and polymerase chain reaction were performed to identify enteroviruses present in the samples. To determine if the results of the study are comparable to the AFP surveillance data, the results of the study were compared to the prevalence and isolation rate among AFP cases of the similar cases collected the same year. Results Prevalence of enteroviruses among healthy children was found to be at 24.7%. Comparing the NPEV rates from the study and AFP surveillance of similar age and the same year of collection, there was no significant difference in NPEV case prevalence.The study identified a total of 19 different enterovirus serotypes with majority belonging to species Enterovirus B (EV-B). Conclusion The study was able to establish a baseline NPEV case prevalence of 24.7% among healthy children aged under 6 years old in three major urban sites in the Philippines. The high isolation of NPEV among healthy children signifies continuous fecal-oral transmission of enteroviruses in the community. Surveillance of other diseases caused by EVs, such as HFMD and meningitis is necessary in order to complete the picture of EV circulation in the Philippines.