The aim of this study was to compare health related quality of life (HRQoL) and assess functional and psychological status in rheumatoid arthritis (RA), fibromyalgia syndrome (FS) patients and controls (each 30 subjects). Demographic characteristics, pain and sleep disturbance by Visual Analog Scale, depression by Beck Depression Inventory (BDI), disease impact by fibromyalgia impact questionnaire, DAS-28, and HRQoL by SF-36 were gathered. The FS group scored significantly worser than the RA group with respect to physical role, social functioning and bodily pain subscales of SF-36. The scores of all SF-36 subscales were significantly lower in FS and RA patients than controls except mental health score. All of the subscales of SF-36 were negatively correlated with BDI scores in FS patients. In RA group, the DAS-28 scores were inversely correlated with all of SF-36 subscales. In conclusion, presence of comorbid depression must be taken into account when determining HRQoL in FS and RA. Essentials improving the HRQoL are management of depression in FS and control of disease activity in RA.