A major cause of diagnostic errors is the underlying complexity caused by patient presentations and the context in which diagnosis is being undertaken. This is especially true for settings like emergency medicine and disease spectrums like infectious diseases. To design artefacts that counter such errors, it is essential to map the factors contributing to diagnostic complexity. However, existing complexity assessment methods in healthcare are limited in scope. Addressing this gap, our work operationalises a complexity estimation tool to identify factors contributing to the diagnostic complexity of 10 infectious disease cases in an emergency medicine setting. Our objective findings are further validated by a strong correlation with the difficulty perceived by attending doctors. The work provides a basis for the design of targeted interventions aiming to mitigate complexity in diagnosis.