•Confirmatory factor analysis indicates that the five-factor dysphoric arousal model best fits the Posttraumatic Stress Disorder Checklist data in the Million Veteran Program.•Multi-group confirmatory factor analyses indicates that the five-factor dysphoric arousal model of posttraumatic stress disorder is noninvariant across genetically identified ancestry and sex (European, African, Ad mixed, and East Asian ancestry.•Multi-group confirmatory factor analyses indicates that the five-factor dysphoric arousal model of posttraumatic stress disorder is also noninvariant across genetically sex (male and female). The Million Veteran Program (MVP) uses the posttraumatic stress disorder symptoms (PTSD) Checklist 17 (PCL-17) self-report to assess PTSD. Existing literature suggests that the five-factor dysphoric arousal model best represents the PTSD symptom clusters; this can be tested within MVP, one of the largest samples collected with suitable data. We compared factor models within MVP across genetically defined subsamples (ancestry European, African, admixed American, and East Asian, sex) via multi-group confirmatory factor analyses in a sample of 279,897 participants. The five-factor dysphoric arousal model best fit the PCL-17 data, consistent with previous findings. The factor structure could also be imposed across all groups tested. Verifying the factor structure provides a framework for future phenotypic and genotypic analyses within MVP and other samples.