Background This longitudinal study aims to compare long-term work disability and absenteeism between anxiety and depressive disorders focusing on the effects of different course trajectories (remission, recurrence and chronic course) and specific symptom dimensions (anxiety arousal, avoidance behaviour and depressive mood). Methods We included healthy controls, subjects with a history of - and current anxiety and/or depressive disorders with a paid job (n=1632). The Composite International Diagnostic Interview was used to diagnose anxiety and depressive disorders and to assess course trajectories at baseline, over 2 and 4 years. The World Health Organization Disability Assessment Schedule II and the Health and Labour Questionnaire Short Form were used to measure work disability and absenteeism. Symptom dimensions were measured using the Beck Anxiety Inventory, the Fear Questionnaire and the Inventory for Depressive Symptomatology. Results A history of - and current anxiety and/or depressive disorders were associated with increasing work disability and absenteeism over 4 years, compared to healthy controls. Long-term work disability and absenteeism were most prominent in comorbid anxiety-depressive disorder, followed by depressive disorders, and lowest in anxiety disorders. A chronic course, anxiety arousal and depressive mood were strong predictors for long-term work disability while baseline psychiatric status, a chronic course and depressive mood were strong predictors for long-term work absenteeism. Limitations Results cannot be generalized to other anxiety disorders, such as obsessive compulsive disorder, posttraumatic stress disorder and specific phobias. Self-reported measures of work disability and absenteeism were used. Conclusions Our results demonstrate that depressive syndromes and symptoms have more impact on future work disability and absenteeism than anxiety, implying that prevention of depression is of major importance.