Background <p>The timely sharing of public health information is critical during a pandemic and is an obstacle that Canada has yet to fully address. During the COVID-19 pandemic, sequencing of the SARS-CoV-2 genome enhanced our understanding of transmission patterns, aided in identifying variants of concern, and supported the development and evaluation of diagnostic tests and vaccines. The Canadian national response faced challenges in aggregating genomic contextual data and carrying out integrated analysis across regions partly due to disparities in COVID-19 case report forms used to capture epidemiological and clinical data that accompanies SARS-CoV-2 sequence data. Such variations delay data integration and make consistent analysis difficult or impossible. The objective of this work was to understand what information was being collected from COVID-19 case report forms used across Canada and identify potential contextual data harmonization issues and solutions.</p> Methods <p>Provincial/territorial/national Canadian COVID-19 case report forms were subjected to field-by-field comparisons to identify variations in data categorization, structures, formats, types, granularity, ambiguity, and questions asked. Federal epidemiologists were consulted to substantiate the results.</p> Results <p>Data harmonization issues and common data elements were identified. We make recommendations for better national coordination, integrated databases, and data harmonization tools.</p> Conclusion <p>This report compares data elements of the various case report forms used across Canada to identify overlaps and differences in the collection method of COVID-19 case information, while also highlighting data harmonization complications and potential solutions. Identifying available data elements will better guide COVID-19 surveillance and research.</p>