In untreated patients with APS, thrombosis recurs in 19-29% of patients per year in the cohort studies reported to date. A systematic review published in 2007 recommended that patients with APS patients should be treated with oral anticoagulants to a target international normalized ratio (INR) of 2.0–3.0 in those with a first-diagnosis of venous thrombosis and to an INR of over 3.0 in those with a first diagnosis of arterial thrombosis.

In 2009, the 5-year-follow-up results of the Euro-Phospholipid Project, a prospective European epidemiologic study designed to identify the main causes of morbidity and mortality in 1000 patients with APS, were released. Over the course of the study, 5.3% of the cohort died, mostly as a result of bacterial infections.

The catastrophic form of APS is characterized by multiple vascular occlusive events mainly affecting small vessels that evolve over a very short period of time (usually, less than 1 week). Patients with catastrophic APS represent less than 1% of diagnosed cases, but they have a high mortality rate of around 50% during the acute event according to the earliest published series. Cerebral involvement is the main cause of death in these patients, being present in 27.2%, followed by cardiac involvement (19.8%) and infection (19.8%). Combined treatment with anticoagulants, corticosteroids and plasma exchanges and/or intravenous immunoglobulins has been associated with a significant decline in the mortality rate.