Several viruses are associated with gastroenteritis in infants. This pilot study, nested within a larger community-based project of early childhood infections, collected daily symptom data and 511 weekly stool samples from five healthy, fully vaccinated, term infants from birth until their second birthday. Real-time PCR assays were used to detect six enteric viruses. Frequent, silent shedding of one or more of the six viruses was observed, particularly involving adenovirus where shedding could be for up to 3 months without gastrointestinal symptoms. These pilot data demonstrate that a positive PCR result for enteric viruses may not always indicate the cause of childhood gastroenteritis.