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Both methotrexate and naproxen can cause problems with the stomach and intestine such as ulcers and further investigation may be needed.  In addition, as you might be aware with all the recent press about Vioxx, non steroidal antiinflammatories (NSAIDs), of which naproxen is one, can increase the risk of heart disease, which may also be the cause of this intermittent chest pain.  Methotrexate is also associated with an increase in cardiovascular risk.  In general, NSAIDs are to be used with caution together with methotrexate as there have been significant interactions noted.  Naproxen is known to be the safest of the bunch, in terms of the interactions.