Circumstantial evidence suggests that the innate immune system and coagulation system share a common evolutionary origin, which explains the extensive crosstalk between inflammatory cytokines and coagulation factors, with many components being important for both systems. This crosstalk has been extensively studied in sepsis, an acute state of high-grade inflammation. However, rheumatoid arthritis (RA) as well as many other autoimmune diseases can also be considered as a prothrombotic state. More and more studies show that autoimmune diseases, including RA, are a risk factor for cardiovascular disease, and also for venous thromboembolic events, such as pulmonary embolism and deep vein thrombosis. Inflammation and its effect on the haemostatic system is probably the link between these diseases. This viewpoint gives an update of the current literature on thromboembolic risk in RA, but also documents important knowledge gaps. This viewpoint will therefore help to focus on further research topics to improve diagnostic and therapeutic options which may relieve both the proinflammatory and the prothrombotic burden of autoimmune diseases.