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Objectives This research was conducted with an aim of determining the correlation between job insecurity and an employee’s work-related health problems among permanent and temporary workers. Methods Using the data from the First Korean Working Conditions Survey conducted in 2006, a total of 7,071 workers, excluding employers and the self-employed, were analyzed. Work-related health problems were categorized as backache, headache, abdominal pain, muscular pain, stress, fatigue, insomnia, anxiety or depression. Each problem was then analyzed for its relationship to job insecurity through logistic regression analysis. Results Among the 7,071 workers, 5,294 (74.9%) were permanent workers and 1,777 (25.1%) were temporary workers. For the permanent workers, presence of high or moderate job insecurity appeared more closely linked to backache, headache, abdominal pain, muscular pain, stress, fatigue, insomnia, anxiety, and depression compared to absence of job insecurity. However, for the temporary workers, only depression appeared to be associated with the presence of high job insecurity. Conclusion The study showed that the presence of job insecurity is correlated with work-related health problems. The deleterious effects of job insecurity appeared to be stronger in permanent than temporary workers. Additional research should investigate ways to effectively reduce job insecurity.