Stroke is a common cause for morbidity and mortality, causing substantial economic costs. Because thrombosis plays a key role in the pathogenesis of ischaemic stroke, heparins, platelet inhibitors and anticoagulants have been used in stroke management. There were high hopes that patients might benefit from the use of heparins. Unfortunately, these expectations have not been met. Instead, thrombolytics have been shown to result in an improvement of outcome in a considerable fraction of patients with ischaemic stroke. Yet, in other areas of stroke management, such as the prevention of venous thromboembolism after stroke, heparins have found their niche. In this review, we report on the currently available literature on heparins for the reduction of stroke-related morbidity and mortality, the prevention of recurrent stroke as well as the prevention of venous thromboembolism in both ischaemic and haemorrhagic stroke with respect to their risks, such as the haemorrhagic transformation of ischaemic strokes.