Objective The aim of the present study was to assess the suitability of emergency department (ED) discharge diagnosis for identifying patient cohorts included in the definitions of key performance indicators (KPIs) that are used to evaluate ED performance. Methods Hospital inpatient episodes of care with a principal diagnosis that corresponded to an ED-defined KPI were extracted from the Queensland Hospital Admitted Patient Data Collection (QHAPDC) for the year 2010-2011. The data were then linked to the corresponding ED patient record and the diagnoses applied in the two settings were compared. Results The asthma and injury cohorts produced favourable results with respect to matching the QHAPDC principal diagnosis with the ED discharge diagnosis. The results were generally modest when the QHAPDC principal diagnosis was upper respiratory tract infection, poisoning and toxic effects or a mental health diagnosis, and were quite poor for influenza. Conclusions There is substantial variation in the capture of patient cohorts using discharge diagnosis as recorded on Queensland Hospital Emergency Department data. What is known about the topic? There are several existing KPIs that are defined according to the diagnosis recorded on ED data collections. However, there have been concerns over the quality of ED diagnosis in Queensland and other jurisdictions, and the value of these data in identifying patient cohorts for the purpose of assessing ED performance remains uncertain. What does this paper add? This paper identifies diagnosis codes that are suitable for use in capturing the patient cohorts that are used to evaluate ED performance, as well as those codes that may be of limited value. What are the implications for practitioners? The limitations of diagnosis codes within ED data should be understood by those seeking to use these data items for healthcare planning and management or for research into healthcare quality and outcomes.