Helicobacter pylori infection is highly prevalent in the human population, yet relatively few infected individuals progress to severe forms of disease, such as peptic ulcers and stomach cancer. The severity of disease outcomes to H. pylori infection is, in large part, determined by inflammatory and cellular responses within the gastric niche that, in turn, are the product of various host, bacterial, and environmental factors. It is now clear that the innate immune system, representing the first line of host defense against infection and other foreign aggressions, is critical to the initiation of the immune responses and inflammation observed in H. pylori infection. We propose that by investigating the activation of innate immune signaling pathways and downstream responses, it is possible to better understand the link between Helicobacter infection and the development of severe disease. Here, we describe tools that have been developed to investigate host innate immune responses to Helicobacter infection.