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Abstract Background Sickness absence is very high in Sweden. The reasons for this phenomenon are not well known. The aim of this study was to investigate the association between degree of self-reported sickness absence and health. The hypothesis was that individuals with long-term sickness absence would report more symptoms and lower self-rated health. Another hypothesis was that women are more likely to self-rate psychiatric diagnoses compared to men, who are more likely to self-rate musculoskeletal diagnoses. Methods The data was obtained with a postal survey questionnaire answered by 43,589 individuals, a Swedish random population sample of men and women aged 18–84 years. The response rate was 65%. This study included 19,826 individuals aged 18–64 years old and still at work. They were divided into four groups, based on the number of reported days of sickness absence during the past year. Results Approximately 40% of the individuals at work mentioned that they had been absent due to illness sometime during the past year. Of those who had been absent 90 days or more, two thirds were women. There was a significant difference between the groups in self-rated health (p < 0.05). Every fifth woman (19.4%) and every fourth man (25.9%) in the group with a sickness absence of more than 89 days rated their health as poor or very poor, but a large proportion, 43.5% of the women and 31.6% of the men, rated their health as good. Long-term illnesses and complaints differed between the groups. The correlations between the groups and illness were mostly significant (p < 0.01). Two thirds of the subjects had both psychiatric and musculoskeletal symptoms. There was a significant difference among them, as men more often had musculoskeletal diagnoses. One third had only psychiatric or musculoskeletal symptoms and in those groups there were no significant diagnosis differences between the sexes. Conclusion Individuals with long-term sickness absence reported more symptoms and lower self-rated health than did those who had not been absent at all, and than those who had been ill 1–28 days. Men and women sick-listed 29 days or more generally reported more illness and complaints. No sex differences among psychiatric and musculoskeletal diagnoses were found, but when reported both psychiatric and musculoskeletal symptoms the musculoskeletal diagnoses were significant among men.