Molecular methods such as real-time polymerase chain reaction (PCR) are rapidly replacing traditional tests to detect fecal viral pathogens in childhood diarrhea. This technique has now increased the analytical sensitivity so drastically that positive results are found in asymptomatic children, leading to complex interpretation of real-time PCR results and difficult distinction between asymptomatic shedding and etiological cause of disease. We performed a review of the literature including pediatric studies using real-time PCR and a minimal inclusion period of one year to exclude bias by seasonality. We searched for studies on rotavirus, norovirus, adenovirus, astrovirus, and sapovirus, known to be the most common viruses to cause gastroenteritis in the pediatric population. For these viruses, we summarized the detection rates in hospitalized and community-based children with clinical symptoms of gastroenteritis, as well as subjects with asymptomatic viral shedding. Moreover, insight is given into the different viral sero- and genotypes causing pediatric gastroenteritis. We also discuss the scoring systems for severity of disease and their clinical value. A few published proposals have been made to improve the clinical interpretation of real-time PCR results, which we recapitulate and discuss in this review. We propose using the semi-quantitative measure of real-time PCR, as a surrogate for viral load, in relation to the severity score to distinguish asymptomatic viral shedding from clinically relevant disease. Overall, this review provides a better understanding of the scope of childhood gastroenteritis, discusses a method to enhance the interpretation of real-time PCR results, and proposes conditions for future research to enhance clinical implementation.