BACKGROUND: Treatment of schizophrenia and major depressive disorder (MDD) with atypical antipsychotics (AAPs) show improved efficacy and reduced side effect burden compared with older antipsychotic medications. However, a risk of treatment-emergent adverse events (TEAEs) remains. TEAEs are hard to quantify and perspectives on the importance of TEAEs differ across patients and between patients and physicians. The current study is a qualitative assessment that investigates TEAEs of AAPs from both patient and physician perspectives to provide better understanding of the occurrence and burden of TEAEs associated with these medications. METHODS: Focus groups comprised of patients with MDD and interviews with patients with schizophrenia were conducted at two qualitative research facilities, along with a physician focus group at one of the facilities. Information collected from patients included an exhaustive list of TEAEs experienced, and the frequency and level of bother of each TEAE; from psychiatrists, information included an exhaustive list of TEAEs based on personal observations and patient report, frequency of TEAEs, clinically important TEAEs, and levels of patient-perceived bother. Standard qualitative analysis methods were used to identify, quantify, characterize, and summarize patterns found in the data collected. RESULTS: A total of 42 patients (25 with MDD and 17 with schizophrenia) and 4 psychiatrists participated in the study. TEAEs reported as bothersome across both patients groups included cognitive issues, weight gain and/or increased appetite, low energy, extrapyramidal symptoms (EPS), and need to sleep/excessive sleep/excessive sleepiness. TEAEs considered more bothersome by patients with schizophrenia were weight gain, low energy, EPS, mental anxiety, and increased positive symptoms; those considered more bothersome by patients with MDD were cognitive issues, somnolence/sedation, and flat/restricted affect. TEAEs considered most clinically important by psychiatrists included metabolic syndrome, weight gain, neutropenia, hyperglycemia, and QT prolongation; those TEAEs considered most bothersome to patients from physicians’ perspectives included weight gain, reduced sexual desire or performance, EPS, akathisia, and hormonal issues. CONCLUSIONS: The wide range of TEAEs that are both frequent and bothersome and the variation in perceived burden according to diagnosis highlight the need for a tailored TEAE-awareness approach when choosing an AAP.