Background Sleep Deprivation (SD) treatment is known for its striking and immediate, but transient effects improving symptoms in 50–70% of patients suffering from depression. SD thus offers the opportunity to study clinical and biological factors preceding and accompanying mood changes and to identify underlying mechanisms of depression. The aim of this naturalistic study was to examine i.) clinical and genetic factors predicting response to SD, ii.) clinical and behavioural changes during the course of SD and iii.) the impact of SD on further course of the disorder. Methods Patients undergoing an episode of major depression (n=78, 34 F/44 M, 71 major depression, 7 bipolar) underwent one night of SD. Depressive symptoms were assessed via standardized expert and self-ratings the day before and up to one month after SD. From the morning prior to SD until the evening after, mood and tiredness were assessed every 2 hours via visual analogue scales, and locomotor activity was concurrently measured via actigraphy. Genome-wide genotyping was carried out using the GSA chip and polygenic risk scores (PRS) were calculated based on genome-wide association data from the PGC MDD consortium. Response to SD was evaluated the day after SD based on global clinical impression (CGI). Logistic regression and mixed models were applied to analyse factors predicting SD and explore the trajectory of changes during and after SD. Results 70% of patients showed immediate antidepressant response. Before SD, responders and non-responders did not differ in self and expert-ratings of depression. A binary logistic regression model found that lower age and later age at disease onset were significantly associated with higher likelihood of response; lower polygenic score for depression, male sex, positive family history of psychiatric disorder and diagnosis of bipolar disorder were associated with increased likelihood response at the trend level. No effects were found for season, diurnal variation, depressive symptom scores and thyroid stimulating hormone levels. Through the course of SD, responders and non-responders differed in mood, with diverging mood trajectories becoming clear the morning and afternoon after SD. Meanwhile, tiredness did not differ between groups. Increased locomotor activity was observed in non-responders in the evening before SD until midnight. Following SD, depressive symptom scores decreased in both groups, but more in responders, in whom the effect was sustained over the entire time of observation. Discussion The current research shows that, in accordance with previous findings, response to SD is associated with specific clinical features and locomotor activity. Furthermore, PRS were examined in this context for the first time, suggesting that a genetic component may contribute to response to SD. In-depth investigation of the underlying causes of these results is a promising approach for future research in depression.