Almost 6% of the Estonian population is not covered by the health insurance system and they have free access only to emergency medical care. The objectives of this study were to provide an overview of the use of medical services by the uninsured, to evaluate the deficit of the services provided to them and to estimate the need for additional funding to gain equal coverage with the insured. The proportion of uninsured persons using hospital and outpatient medical services is 2–3 times lower than it is among the insured, and those uninsured who use the services do so considerably less often. The major health problems not addressed among the uninsured are metabolic and musculoskeletal disorders, sexually transmitted diseases and follow-up of injuries. Taking into account that in the Estonian health insurance system uninsured persons are in average healthier compared to the insured, the total additional funding needed to guarantee equitable access to the whole population in Estonia can be estimated at 100–150 million kroons per year.