The recent emergence of West Nile virus (WNV) in the western hemisphere has been marked by an increase in severe neurological disease. The factors that contribute to this increase in pathogenicity are poorly understood, however, there is evidence that the host antiviral response plays a significant role in controlling WNV mediated disease. The innate antiviral response is mediated by a variety of pathogen recognition receptors, including RIG-I. Here, we analyzed the RIG-I mediated antiviral response to WNV infection. We identified multiple regions of the pathogenic WNV-NY genome and antigenome that act as pathogen associated molecular patterns (PAMPs) capable of stimulating the RIG-I response. Additionally, preliminary examination of the related, non-pathogenic WNV-MAD78 genome has revealed stimulatory regions that differ from those found in the WNV-NY genome. One of PAMP region, the 5'UTR, was analyzed further to elucidate the secondary structural elements present in the RNA, which may be contributing to the antiviral response. Similar, equally stimulatory structures were found in the 5'UTR of both the WNV-NY strain WNV-MAD78, indicating similar structures may be recognized for RIG-I activation. We also examined the role of DDX3, a DExD/H box helicase similar to RIG-I, in WNV infection. DDX3 appeared to co-localize with WNV protein and DDX3 expression was reduced at late points in infection, but DDX3 overexpression had no effect on viral replication or protein expression. Therefore, the exact role that DDX3 plays during the course of WNV infection remains unresolved. Taken together, our data suggests a specific structural requirement to activate the RIG-I mediated antiviral response.