Background Back pain and neck pain are leading causes of the burden of disease worldwide, while information about their prevalence in Russia is missing. Methods The population-based Ural Eye and Medical Study was conducted in a rural and urban region in Bashkortostan/Russia. As part of a detailed systematic examination, we assessed the prevalence of low back pain, thoracic spine pain and neck pain in an interview with standardized questions in 5397 study participants (mean age:58.6 ± 10.6 years;range:40–94 years). Results The mean prevalence of low back pain, thoracic spine pain and neck pain was 2912/5397 (54.0%;95% confidence interval (CI):52.6,55.3), 1271/5397 (23.6%;95%CI:22.4,24.7), and 1570/5397 (29.1%;95%CI:27.9,30.3), respectively. A higher prevalence of low back pain was associated with females (P = 0.04;odds ratio (OR):1.14;95%CI:1.004,1.30), younger age (P < 0.001;OR:0.99;95%CI:0.98,0.99), higher body mass index (P = 0.002;OR:1.02;95%CI:1.01,1.03), lower frequency of vigorous activities during leisure time (P = 0.001;OR:0.79;95%CI:0.69,0.90), more time spent sitting and reclining (P = 0.03;OR:1.00;95%CI:1.00,1.00), higher serum concentration of high-density lipoproteins (P = 0.004;OR:1.10;95%CI:1.03,1.18), higher prothrombin index (P = 0.003;OR:1.01;95%CI:1.003,1.01), higher prevalence of a history of cardiovascular disease (P = 0.004;OR:1.23;95%CI:1.07,1.42), falls (P < 0.004;OR:1.71;95%CI:1.45,2.00), bone fractures (P = 0.01;OR:1.18;95% CI:1.03,1.34), unconsciousness (P < 0.001;OR:1.78;95%CI:1.40,2.25), osteoarthritis (P < 0.001;OR:2.76;95%CI:2.34,3.26), iron-deficiency anemia (P < 0.001;OR:1.87;95%CI:1.41,2.50), and thyroid disorder (P = 0.004;OR:1.37;95%CI:1.10,1.70), fewer days of vegetable intake (P < 0.001;OR:0.89;95%CI:0.85,0.93), smaller amounts of salt intake (P = 0.008;OR:0.97;95%CI:0.94,0.99), higher anxiety score (P < 0.001;OR:1.05;95%CI:1.03,1.06), and in women, history of menopause (P = 0.02;OR:1.36;95%CI:1.05,1.75). The prevalence of thoracic spine pain and neck pain showed similar associations. Conclusions In a Russian population, the prevalence of low back pain, thoracic spine pain and neck pain (54.0, 23.6 and 29.1%, respectively) were correlated with parameters such as the female sex, younger age, higher body mass index, higher anxiety score, higher prevalence of a history of cardiovascular disease, lower frequency of vigorous activities and more time spent sitting or reclining. These data may be of interest for assessing the burden of back and neck pain in Russia as part of the global burden of disease.