Objective. To compare the frequency and correlates of sexual dysfunction in patients with Major Depressive Disorder on SSRI treatment with those who are not. Methods. Patients diagnosed with Major Depressive Disorder, without comorbid psychopathology/medical disorder/alcohol/nicotine use for the past year with a CGI-S severity score of 4 were included. Two groups were formed, one using SSRIs at least for 6 weeks before the study, and another who were free of drugs for the last month. Arizona Sexual Experience Scale (ASEX) was given to determine sexual dysfunction. P was set at 0.05. Results. Thirty-three patients (25 female, 75.8%) were included. The study group was using sertraline (n = 10, 52.6%) and citalopram (n = 9, 47.4%). Fourteen patients on SSRIs (73.7%) and 12 controls (% 85.7) displayed sexual dysfunction with no difference between groups. Female gender was associated with sexual dysfunction, regardless of treatment (P = 0.04). Arousal sub-test of ASEX differed significantly in the group with dysfunction (P = 0.04). Conclusions. Female gender may be a risk factor for sexual dysfunction in the presence of depression, regardless of drug use. Arousal may be affected in patients, regardless of treatment, and this may reflect the effect of depressive cognitions on libido.