The capacity of any organization to be prepared for a public health threat is influenced in part by the system in which the organization is located, just as the preparedness of the overall system can be influenced by the strengths and weaknesses of any single organization. The cross-case and intra-provincial comparative design allows our research to discriminate among different system elements and examine the independent influence of organizational attributes, institutional environments, and inter-organizational networks on public health preparedness. In addition, the mixed methods approach enables our research to analyse the role of both informal and formal relationships in the emergence of inter-organization networks and the development of prepared and responsive public health systems. As far as we are aware, our project is one of the first to assess public health preparedness at the systemslevel while accounting for the critical role that inter-organizational relationships play in the emergence of a cohesive and responsive system. Moreover, in deciphering the independent influence of inter-organizational ties within the overall system, the research will provide measures that will help researchers and policy-makers evaluate the degree of coordination among organizational actors.