Abstract Background The increasing prevalence and incidence of autoimmune and respiratory diseases is a leading public health concern. This study aims to quantify the public health and broader economic gains from treating autoimmune and respiratory diseases in Greece. Methods A decision-analytic model was constructed evaluating the socioeconomic and fiscal gains of established standard of care treatments against 4 autoimmune disorders namely, rheumatoid arthritis, psoriatic arthritis, psoriasis, ankylosing spondylitis and against the respiratory diseases of asthma, and COPD. Morbidity reductions from treatment were translated into averted loss of income and absenteeism and averted tax revenue loss and prevented disability pensions. Targeted literature reviews were conducted to obtain the effectiveness of treatments on productivity-related outcomes. Economic data were obtained from official sources. Results Treating 1,000 patients for the autoimmune and respiratory conditions is estimated to generate annual gains of 196.3 productive life years (PLYs), to avert 48,547 absenteeism days and to prevent 1.2 disabilities. The annual socioeconomic and fiscal gains of treatments against autoimmune disorders are estimated at €6.5 million and €1.3 million, respectively. Preventing asthma and COPD-related morbidity, among 1,000 patients, is estimated to yield annual socioeconomic gains of €1.2 million and fiscal gains of €0.4 million. Conclusions Effective treatment of autoimmune and respiratory diseases may generate substantial public health, socioeconomic and fiscal gains, simultaneously promoting population’s health and the sustainability of the healthcare system. Key messages • It is the first study carried out in Greece aimed to assess the positive impact on public health and the broader economic value of treating autoimmune and respiratory diseases. • Therapeutic value of pharmacological interventions transcends the potential benefits to patients and public health.