In this study, we evaluated the prevalence of fibromyalgia (FM) in iron deficiency anemia (IDA) and thalassemia minor (TM) patients and associated factors. In addition, we investigated the prevalence of IDA in outpatients with fibromyalgia, and its effect on clinical findings. The study included 205 IDA, 40 TM patients and 100 healthy controls. FM was diagnosed according to 1990 ACR criteria. Whole blood count, biochemical tests, and serum iron parameters were determined. Pain, fatigue, and FM Impact Questionnaire (FIQ) functional item scores were assessed in FM subjects. In addition, the prevalence of IDA in FM patients diagnosed at the Rheumatology Outpatient Clinic was determined. The prevalences of FM in IDA (17.6%) and TM (20%) groups were higher than in controls (6%; p values 0.006 and 0.025, respectively). When IDA patients with FM were compared to those without FM, it was seen that a higher percentage were females, married, and a higher percentage had history of pica (all p values < 0.05). Serum hemoglobin and iron parameters did not differ between IDA patients with and without FM. IDA was detected in 48 (24.5%) of 196 FM patients. FM patients without IDA had higher sleep disturbance scores (p = 0.012) and longer duration of FM (p = 0.045). FM was a common finding in patients with IDA and TM. FM was associated with female sex and history of pica in IDA patients, and not associated with serum hemoglobin and selected iron parameters. The presence of FM in TM had no association with any of the above-mentioned parameters.