Recent research has shown that patients undergoing hematopoietic SCT (HSCT) experience multiple symptoms that can affect the sleep quality adversely. This study investigated the sleep quality of patient in the acute course of HSCT, and measured the impact of sociodemographic, medical, physical and psychological factors. Fifty patients were assessed before admission, 44 participated during inpatient treatment and 32 on day 100 (+/-20) post-transplantation. Measuring instruments included the Pittsburgh Sleep Quality Index (PSQI) and a sleep diary (sleep quality), the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (health-related quality of life), the Hospital Anxiety and Depression Scale-German version (anxiety/depression) and the German version of the Cancer and Treatment Distress Scale (treatment-specific distress). The prevalence of sleep disturbances was 32% before admission, 77% during the hospital stay and 28% after discharge. Difficulty in maintaining sleep was the most intense sleep problem during the inpatient phase. This was mainly caused by disturbing noises and need to use the bathroom frequently. Sleep problems were significantly worse during the hospital stay compared with the other measurement points in time (P<0.001). A significant interaction was seen between the time course of sleep disturbances and the type of transplantation (P=0.001). The findings suggest that sleep disturbances after HSCT are particularly associated with physical functioning, fatigue and treatment-specific distress, and factors that contribute to sleep difficulties in the general population seem to be less important.