Abstract Background Estonia, a small country defined by NUTS2 regions, faces challenges in assessing health disparities across its different counties when using global health data such as the Global Burden of Disease (GBD). Recognizing this limitation, Estonia initiated independent burden of disease studies in Estonia since 2013, with the findings being biennially published through the health statistics database of the National Institute for Health Development. The objective of this research is to assess the strengths and limitations inherent in various methods when calculating the years of life lost due to premature mortality (YLLs). Methods The approach to assess the burden of disease in Estonia differs somewhat from the Global Burden of Disease (GBD) methodology. One key distinction lies in our utilization of a national life expectancy table and our presentation of results at the LAU1 regional level. These burden of disease studies utilize region-specific life tables supplied by Statistics Estonia, categorized by county and gender, to compute Years of Life Lost (YLLs), offering an opportunity to pinpoint and tackle regional health issues. Results Since the calculation of YLL (Years of Life Lost) in these past studies has relied upon Estonia’s regionalized life tables, categorized by county and gender, the results exhibit substantial disparities when juxtaposed with the Global Burden of Disease study conducted by the Institute for Health Metrics and Evaluation (IHME). Conclusions This research aims to delve deeper into these variations, examining the challenges related to methodology, the availability, and the quality of data, and most importantly, knowledge translation. Our own burden of disease studies empowers us to formulate informed policy recommendations precisely tailored to the distinctive needs of each county, thereby facilitating targeted interventions, and driving improvements in overall public health outcomes.