The main adverse effects of heparin therapy are bleeding, thrombocytopenia (decrease in blood platelet count) and osteoporosis (reduction in bone mass, leading to fractures). Patients who have a risk of complications are those who have had recent surgery and those who have peptic ulcers, malignancy, liver disease, hemostatic defects (reduced blood clotting ability), and those who are overweight, over 65 years, and female. 

Bleeding. Control of bleeding depends on the following locality and severity of the bleeding, risk of recurrent thromboembolism (clotting), and aPTT measurements. First, heparin is stopped temporarily or permanently. A vena cava filter may be inserted. Protamine sulfate may be used to reverse the effects of heparin, if necessary.

Thrombocytopenia. Platelet count falls 5 to 10 days after heparin is started in about 1–2% of patients. The count either falls to lower than the normal range or decreases by 50%. A very small percentage of patients (0.1–.2%) may experience arterial or venous thrombosis, which may lead to limb amputation or death. Heparin is stopped immediately. The physician will prescribe alternative drugs for those who require ongoing anticoagulant therapy.

Osteoporosis. Bone mass may be reduced in patients receiving 20,000 units heparin/day for over 6 months. This may not be entirely reversible.