As per the agreement, Cordis will receive $1.7bn from Boston Scientific and Johnson & Johnson expects to record the majority of this payment as a special item in the first quarter of 2010.
Boston Scientific will pay Cordis $1bn by close of business on February 1, 2010, and $725m on January 3, 2011.
The disputes involved several coronary stent products including Cordis's Cypher stent and Boston Scientific's Liberte, Taxus Liberte and Taxus Express stents.
Seth Fischer, group chairman of Cordis, said: "We are very pleased to resolve these long-standing patent disputes."
Reportedly, other litigation between the two companies will not be affected by this settlement, including the Cordis lawsuits against Boston Scientific's Promus Stent products.