To make rehabilitation of musculoskeletal disorders effective it is crucial to identify circumstances that tend to support the persistence of sickness absence. A total of 93 patients with recently developed disorders in the neck and shoulders were followed for one year after rehabilitation, in order to identify factors associated with recovery and chronicity, respectively. Health status was evaluated before rehabilitation and after 12 months in terms of sickness absence, pain ratings and self-rated quality of life, the Sickness Impact Profile. The study group was divided into tertiles based on their number of days of sickness absence during the follow-up period (short: < 25 days, medium: 25-101 days, long: > 101 days). Those with long-term sickness absence perceived higher physical and mental load in their jobs. There was also a higher proportion of persons who were not born in Sweden in this group and on average they had more sick-leave days the preceding year. Other background characteristics and personality ratings were similar between the groups. Long-term sickness absence was associated with worse ratings in quality of life after one year, and pain did not diminish during the follow-up year. Multiple regression analysis indicated that long-term sickness absence was largely associated with work conditions rather than with individual characteristics. Therefore, the results underscore the importance not only of treating the individual with musculoskeletal disorders, but in particular of improving his or her work conditions.