BACKGROUND Treating diabetes mellitus type 2 (DMT2) essentially involves long-term changes of health behaviour, especially diet and physical activity habits. Medical rehabilitation tries to support these changes by patient education and practical instructions. While short-term successes are frequently obtained, the main challenge lies in maintaining these results in the longer run. This study examines whether a fractionated inpatient rehabilitation programme of 3 weeks duration in combination with an additional week of inpatient rehabilitation after 6 months and a subsequent aftercare telephone service facilitates positive long-term effects for patients with DMT2. METHODS A prospective randomized controlled trial was conducted with 411 patients with DMT2 in order to compare the fractionated inpatient rehabilitation programme with aftercare to a 3-weeks standard rehabilitation programme without aftercare. The analysis included physiological (cardiovascular risk, HbA1c, BMI) and psychosocial (diabetes-specific coping, quality of life) parameters at baseline (beginning of the programme) and 1 year later. RESULTS After 12 months, no significant differences between the groups were found in the physiological parameters. At the same time, however, the aftercare group showed larger benefits in almost every psychosocial dimension (coping, quality of life, subjective health). Coping and quality of life had even improved when compared to baseline. In contrast, these parameters had decreased further in the standard-care control group when compared to baseline. CONCLUSIONS The intensive aftercare was successful in the long-term improvement of the patients' psychological well-being. Also, the high rate of participation in fractionated inpatient rehabilitation suggests both the acceptance of and the need for aftercare. However, positive long-term changes of physiological parameters probably will require more specific interventions or individual case management. The effectiveness of fractionated inpatient rehabilitation may be limited by the adverse social, psychological and financial situation of the patients.