With the success of high dose therapy supported by autologous bone marrow transplantation (ABMT) for malignant lymphomas, medical late-effects and secondary effects on subjective health, like fatigue, are of concern. Fatigue is poorly understood and correlates have been barely addressed. Health-related quality of life (HRQL), fatigue, and correlates to fatigue, including endocrinological status and serum levels of interleukin-6, tumor necrosis factor, and soluble tumor necrosis factor receptors, were investigated in a cross-sectional study of 33 lymphoma patients (median age 39 years) 4-10 years after ABMT. The survivors were compared to general population norms. Fatigue was highly prevalent, and females reported significantly more fatigue and impaired HRQL compared to males and the normal population. Gonadal dysfunction was found in the majority of the patients, but no statistically significant endocrinological or immunological associations with fatigue could be demonstrated. The high level of fatigue among female long-term survivors after ABMT may be related to the gonadal dysfunction, but further studies of possible mechanisms behind fatigue are necessary.