For many years in Russia, apatite ore mining has been associated with high levels of occupational morbidity. The aim of the study was to retrospectively assess occupational disease trends in Russian Arctic apatite miners. We analysed data from routine health screening of 2 649 underground apatite miners in 2007 and data of social-hygienic monitoring “Working conditions and occupational morbidity” in 2008–2020. In 2007, according to the results of routine health screening, 6 778 chronic diseases were diagnosed in 2 649 miners, the most prevalent being musculoskeletal (34.4%) and eye (16.0%) diseases. In the next 13 years, 572 occupational diseases were first diagnosed in 300 (11.3%) miners, most prevalent being musculoskeletal diseases (47.2%). The risk of developing occupational diseases in tunnellers exceeded that in all other miners, including timber-men (RR = 1.56; CI 1.06–2.30), vibration-loading machine operators (RR = 1.67; CI 0.99–2.80), drillers (RR = 1.51; CI 1.08–2.11) and blasters (RR = 2.12; CI 1.55–2.84). We conclude that ongoing modernisation of ore mining processes and medical preventive measures should include more effective health-improving interventions for underground apatite miners. Findings from the analysis of data can be used by health professionals and policy makers to address these problems.