The prevalence of atrial fibrillation is high and comparable in both sexes. Such factors as differently expressed blood biomarkers in women and men may play a role in the occurrence of atrial fibrillation and the development of thrombotic complications. To study markers of inflammation and platelet activation in patients with atrial fibrillation of non-valvular origin, receiving anticoagulant therapy and having a history of thrombotic complications and patients with atrial fibrillation without thrombotic complications, depending on the gender of the patients. The study included 22 healthy volunteers and 60 patients diagnosed with atrial fibrillation receiving anticoagulant therapy, of which 21 patients developed thrombotic complications. Serum levels of α2- macroglobulin, hsC-reactive protein, fetuin A, α-1-acid glycoprotein, L-selectin, serum amyloid P, adipsin, and platelet factor 4 were studied on FLEXMAP 3D using Acute Phase diagnostic test systems Panel 3. A comparative study of the content of biomarkers demonstrated an increased concentration of C-reactive protein in men and women in both groups of patients with atrial fibrillation; decrease in fetuin A and L-selectin in the group of women with thrombosis compared with women without thrombotic complications and compared with healthy women. There were no gender differences in the concentration of fetuin A and L-selectin in the group of patients with atrial fibrillation without thrombotic complications and in healthy volunteers. The level of adipsin had no gender differences in the group of patients with atrial fibrillation with thrombosis and in healthy volunteers, however, it was significantly increased in women without thrombosis. The content of platelet factor 4 in women in both groups of patients exceeded the value of this indicator in healthy women; no gender differences were found in the groups of patients with atrial fibrillation. Low levels of fetuin A and L-selectin, with a simultaneous increase in C-reactive protein and platelet factor 4, lead to an increase of prothrombogenic potential and to a change in the balance of pro- and antiinflammatory mediators towards increased inflammation in female patients with atrial fibrillation.