Abstract 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