Doctors often undertake patient diagnosis in emergency settings in ambiguous, uncertain and stressful conditions. Such conditions along with the inherent factors associated with patient presentations generate complexity towards accurate diagnosis. To design effective interventions that aid the diagnostic decision-making of doctors, there is a need for designers and human factors experts to map these contextual and case-specific complexity factors associated with patient cases. Addressing this need, the study demonstrates the operationalisation of a protocol to objectively assess the contextual and case-specific complexity factors of patient cases. The work is the result of a week-long pilot study at the All India Institute of Medical Sciences (AIIMS), New Delhi. Our findings revealed the protocol to be successful in identifying the complexity factors associated with seven patient cases and differentiating them based on a complexity score. The general trend of complexity was also confirmed qualitatively by collaborating doctors. Further refinements are suggested for future work.