Although burnout and mental health problems may adversely impact quality of scientific research, academic productivity, and attrition in biomedical doctoral training programs, very little research has been done on this topic. Recent studies have used brief survey methods to begin to explore burnout and mental health problems in biomedical doctoral students. In this pilot study, biomedical doctoral students (N = 69; 12% of enrolled biomedical doctoral students at a large research institution's school of medicine in the United States) were administered standardized psychiatric interviews and self-report questionnaires focused on dimensions of burnout, mental health symptoms, and academic outcomes. We discovered high levels of burnout, depression, and anxiety. Additionally, we identified that burnout was significantly associated with thoughts related to dropping out, subjective appraisal of employment opportunities, functional impairment due to a mental health problem, and having at least one current psychiatric disorder. These findings extend prior research indicating the presence of significant emotional health challenges doctoral students in biomedical graduate programs face involving high burnout and difficulties with the training environment. We outline several recommendations and next steps to programmatically understand and address these emerging emotional wellness concerns in biomedical doctoral students.