Emotional Intelligence (EI) is a broad personality construct signifying the ability to perceive and to regulate affects within oneself. Alexithymia is another personality construct denoting difficulty in identifying and expressing emotions, with an externally oriented thinking style. Although previously considered to be independent, some studies have shown that these constructs overlap. The aim of this study was to evaluate and compare the levels of EI and alexithymia in patients with panic disorder, major depressive disorder (MDD), and generalized anxiety disorder (GAD). The subjects included 171 psychiatric patients and 56 non-clinical controls. Psychiatric diagnoses were based on DSM-IV criteria. The Emotional Intelligence Scale-34 (EIS-34) and the Toronto Alexithymia Scale (TAS-20) were used to assess EI and alexithymia. All three patient groups scored statistically significantly higher than the non-clinical controls on TAS-20 total score and the TAS-20 subfactors of difficulty identifying feelings and difficulty describing feelings. EIS-34 scores were lower in patient groups than in the non-clinical controls, but only the EIS-34 intrapersonal subscale was significant difference. Total TAS-20 and EIS-34 scores in the patient cohort were inversely and significantly correlated These results reaffirm an overlap between EI and alexithymia with the intrapersonal factor of EI to be more dependent on the difficulty identifying feelings dimension of alexithymia in subjects with MDD and GAD.