IntroductionWith the lowest life expectancy in the Balkans, underlying causes of morbidity in Kosovo remain unclear due to limited epidemiological evidence. The goal of this cohort is to contribute epidemiological evidence for the prevention and control of non-communicable diseases such as depression, hypertension, diabetes and chronic respiratory disease in Kosovo as the basis for policy and decision-making, with a spotlight on the relationships between non-experimental primary healthcare (PHC) interventions and lifestyle changes as well as between depression and the course of blood pressure.Methods and analysisPHC users aged 40 years and above were recruited consecutively between March and October 2019 from 12 main family medicine centres across Kosovo. The data collected through interviews and health examinations included: sociodemographic characteristics, social and environmental factors, comorbidities, health system, lifestyle, psychological factors and clinical attributes (blood pressure, height, weight, waist/hip/neck circumferences, peak expiratory flow and HbA1c measurements). Cohort data were collected annually in two phases, approximately 6 months apart, with an expected total follow-up time of 5 years.Ethics and disseminationEthical approvals were obtained from the Ethics Committee Northwest and Central Switzerland (Ref. 2018-00994) and the Kosovo Doctors Chamber (Ref. 11/2019). Cohort results will provide novel epidemiological evidence on non-communicable diseases in Kosovo, which will be published in scientific journals. The study will also examine the health needs of the people of Kosovo and provide evidence for health sector decision-makers to improve service responsiveness, which will be shared with stakeholders through reports and presentations.