Current approaches to studying the ecology and evolution of infectious disease systems have provided substantial theoretical development and data during the past decades. However, it is evident that in many cases, the rate at which we are generating substantial new knowledge is slowing. Our ability to understand higher level interactions that influence the patterns of diseases in the real world remain insufficient to allow us to predict outcomes and devise interventions that minimally impact the ecosystem. It has been proposed that a distributed research facility such as NEON could push the field of infectious disease ecology beyond what is possible based on our current research capabilities. With this in mind, a workshop was convened to identify the major questions in the ecology and evolution of infectious disease systems that could best be addressed by NEON, so that the scientific requirements of those questions can inform the infrastructure needs for an infectious disease component of NEON. This document highlights the design recommendations that resulted from discussions at the NEON infectious disease workshop.