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I took methotrexate for three months. I started having breathing problems ie coughing and shortness of breath. At first I thought it was a really bad cold. Another doctor thought I had developed Asthma. I went in to see my Doctor on for my normal monthly check up and he said I was having an allergic reaction to the methotrexate. Question: How long will it take for my breathing to go back to normal? It has been two weeks and I am still having problems breathing...even with the asthma meds. There is a lot of junk in my lungs.