Fibromyalgia (FM) is characterized by a chronic widespread pain, general fatigue, anxiety, depression, sleep disturbances and functional disorders. FM affects both women and men in 9:1 to 20:1 ratio. The purpose of this clinical study is to analyze clinical manifestations in patients with primary and secondary fibromyalgia. Eighty-three patients with primary FM, 39 patients with FM and osteoarthritis (OA), 23 patients with FM and systemic lupus erythematosus (SLE), 27 patients with SLE, and 36 healthy subjects were included. The present study compared chronic pain, fatigue, depression and anxiety in patients with primary FM, patients with SLE, FM + OA, FM + SLE and healthy subjects. Based on the 2016 criteria for number of chronic widespread pain areas, there is a statistically significant difference of the control group compared to the patients with primary FM (p = 0.001), FM + OA (p = 0.001), FM + SLE (p = 0.001), SLE (p = 0.001). Based on the MFIS fatigue scale, the chronic fatigue is a statistically significant difference of the control group, as compared to patients with primary FM (p = 0.004), FM + OA (p = 0.02), FM + SLE (p = 0.001). Based on the HADS clinical parameter, anxiety and depression are a statistically significant difference of the control group, as compared to patients with primary FM (p = 0.01), FM + OA (p = 0.01), FM + SLE (p = 0.01), and no difference in patients with SLE (p = 0.77). The comparison between the patient groups is important to evaluate the disease activity and the treatment to be recommended.