Despite the commitment of federal and provincial agencies in Canada to improve public health system performance and develop overall public health preparedness, little is still known about the current systems-level state of public health preparedness in Canada. While coordination is seen as a necessary element for public health preparedness, few measures of inter-organizational collaboration relevant to public health preparedness have been developed and assessed in relation to other features of the organizational and inter-organizational environment. This study protocol presents the premises, conceptual model and methods used to measure and assess public health preparedness in Alberta, Canada. Although provincial public health agencies are themselves embedded within federal and global public health preparedness systems, we focus primarily on the organizational environment of public health preparedness in Alberta so as to develop contextually-relevant measures and evaluation techniques as well as address issues related to potential cross-Alberta variations in public health preparedness.