Noroviruses are major causative agents of sporadic and outbreak-associated nonbacterial gastroenteritis worldwide. Real-time RT-PCR has rapidly become the principle means for norovirus detection due to its sensitivity and specificity; however sequence variations in the Norovirus genome can cause problems for real-time chemistries. Using a combination of modified bases and minor groove binder-conjugated Eclipse hybridization probes, a one step real-time RT-PCR assay was designed and optimized to detect norovirus genogroups I and II. Additionally, an RNA internal control was incorporated into the assay to monitor nucleic acid extraction and amplification inhibition. As part of this study, a combination of 36 stool and RNA samples were tested and results were compared to a previously described TaqMan assay. An overall correlation of 97% was obtained. After 7 months of clinical testing, a percent positive rate of 39% was determined, with genogroup II accounting for 98% of the positives. Overall, the Eclipse assay is a sensitive and robust method for detecting and typing norovirus genogroups I and II as well as useful for routine clinical testing. Incorporating modified bases helps overcome design limitations due to single nucleotide polymorphisms.