Background: Cognitive dysfunction in unipolar disorder (UD) and bipolar disorder (BD) may persist into remission and affect psychosocial function. Executive and memory deficits during remission may be more pronounced in BD than UD. However, patients' subjective experience of cognitive difficulties is poorly understood, and it is unclear whether BD and UD patients experience different cognitive difficulties. Aims: To investigate whether there are differences in the quality and magnitude of subjective cognitive difficulties between UD and BD, and which factors influence the subjective cognitive difficulties in these patients. Methods: Patients with BD (n = 54) or UD (n = 45) were referred to the outpatient mood disorder clinic at Department of Psychiatry, Copenhagen University Hospital, following hospital discharge. Affective symptoms and patients' experience of cognitive symptoms were assessed at their initial consultation at the clinic. Results: Patients experienced mild to moderate cognitive impairment despite being in partial or full remission, but there were no differences in subjective difficulties between BD and UD. Subjective cognitive dysfunction was predicted by depression severity, anxiety and mania symptoms rather than by diagnosis, age, gender or alcohol misuse. Conclusion: The absence of difference in subjective cognitive difficulties between UD and BD contrasts with evidence of greater objective dysfunction in BD. This highlights a potential discord between subjective and objective measures of cognitive function. Subjective cognitive function was predicted by affective symptoms, perhaps suggesting that this reflects mood symptoms rather than objective deficits. This points to a clinical need for objective assessment of cognitive function in these patient groups.