Objectives: The study purpose was to describe the Swedish HealthPhys cohort. Using data from the HealthPhys study, we aimed to describe the prevalence of clinical burnout and major depression in a representative sample of Swedish physicians across gender, age, worksite, hierarchical position, and speciality in spring of 2021, during the third wave of the Covid-19 pandemic. Method: The HealthPhys questionnaire was sent to a representative sample of practising physicians (n = 6699) in Sweden in February to May of 2021 with a 41.3% response rate. The questionnaire included validated instruments measuring psychosocial work environment and health including measurements for major depression and clinical burnout. Results: Data from the HealthPhys study showed that among practising physicians in Sweden the prevalence of major depression was 4.8% and clinical burnout was 4.7%. However, the variations across sub-groups of physicians regarding major depression ranged from 0% to 10.1%. For clinical burnout estimates ranged from 1.3% to 14.5%. Emergency physicians had the highest levels of clinical burnout while they had 0% prevalence of major depression. Prevalence of exhaustion was high across all groups of physicians with physicians working in emergency departments, at the highest (28.6%) and anaesthesiologist at the lowest (5.6%). Junior physicians had high levels across all measurements. Conclusions: In conclusion, the first data collection from the HealthPhys study showed that the prevalence of major depression and clinical burnout varies across genders, age, hierarchical position, worksite, and specialty. Moreover, many practising physicians in Sweden experienced exhaustion and were at high risk of burnout.