Little is known about secondary impairments and overuse problems in patient with acquired or congenital upper limb deficiency. Our aim was to estimate the frequency of overuse problems in persons after unilateral upper limb deficiency and identify the factors relevant for development of these problems. Cross-sectional study conducted at the University Rehabilitation Institute in Ljubljana. In total, 65 persons after unilateral upper limb deficiency who had visited our subspecialist outpatient clinic during the 2011-2013 period (excluding those with other possible medical causes of overuse-type problems) were interviewed about the frequency, duration and severity of neck, elbow and shoulder pain and the presence of carpal tunnel syndrome and filled in the Orthotics and Prosthetics User Survey-Upper Extremity Functional Status questionnaire. The most frequent problem was carpal tunnel syndrome, followed by shoulder pain, neck pain and elbow pain. No statistically significant association of deficiency level, cause of deficiency, time since deficiency, extent of daily prosthesis use or type of prosthesis with frequency or severity of pain or number of problems was found. The presence of carpal tunnel syndrome decreased from wearing no prosthesis through aesthetic and body-powered to myoelectric prosthesis (p = 0.014). Factors contributing to overuse problems after upper limb deficiency are not straightforward, so a large multicentric study is warranted. Persons with acquired or congenital upper limb deficiency are under a heightened risk of developing overuse problems but the contributing factors are not clear, so regular individual follow-up is required.