Aims. To investigate recognition of diagnostic overshadowing, i.e., misattribution of physical symptoms to mental illness, among emergency medicine professionals; further, to identify contributory and mitigating factors to diagnostic overshadowing. Methods. In-depth individual interviews of 25 emergency department clinicians and qualitative analysis using thematic analysis. Results. Diagnostic overshadowing was described as a significant issue. Contributing factors included: (1) problems of knowledge and information gathering; (2) clinicians' attitudes toward people with mental illness, substance misuse and frequent attenders; and (3) difficulties in working with mental health services in the context of a 4-h target for discharge from the emergency department. Avoidance of patients with a psychiatric diagnosis was also described, due to fear of violence. Conclusion. The physical health care of people with mental illness in emergency departments may be adversely affected by diagnostic overshadowing and avoidance by clinical staff, along with difficulties created by the illness, medication and the emergency department environment. Greater joint working between psychiatric and emergency department staff is suggested as one way to reduce diagnostic overshadowing.