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Objectives: The diagnosis of depression is based on a highly variable set of symptoms. Therefore, depression should not be viewed as single disease, but a heterogenous syndrome comprised of different pathophysiologies. There are several subtypes of depression which already incorporated in DSM-IV. This article provides a systematic review of pharmacological treatments of two recognized subtypes of depression-dysthymic disorder and atypical depression. Methods: Systematic search of relevant literatures on dysthymic disorder and atypical depression was performed by proposed search strategy of the Clinical Research Center for Depression of Korean Health 21 R&D Project. All identified literatures carefully reviewd and classified according to SIGN grading system and summarized in a narrative manner.Results: For the treatment of dysthymia and atypical depression, selective serotonin reuptake inhibitors(SSRIs) and moclobemide have more evidence than the other antidepressants. SSRIs and moclobemide showed superior tolerability than tricyclic antidepressants. Conclusions: The authors proposed treatment recommendations for dysthymic disorder and atypical depression by the methods of evidence-based medicine(EBM). However, guideline developing methods of EBM also have several inevitable limitations. Therefore, in the absence of clear and significant differences in efficacy, the choice of medication must be individualized for a particular patient based on psychiatrist's own clinical decision.