Hi Mini,
Reading your post, I get the impression that your GI doc thinks that he can actually "cure" MC. As most of us here have discovered, MC cannot be cured, it can only be controlled. (Of course, it can be controlled very effectively, but it requires continuous treatment, not a high dose of meds followed by a few days of remission, and then the symptoms return, and the cycle starts all over again).
If the Entocort is controlling your symptoms, you would be much better off, (as far as your long-term health is concerned), if you remained on a maintenance dose of Entocort, rather than switching to methotrexate. This quote pretty well sums up my opinion of methotrexate:
Methotrexate may cause very serious side effects. Some side effects of methotrexate may cause death. You should only use methotrexate to treat life-threatening cancer, or certain other conditions that are very severe and that cannot be treated with other medications. Talk to your doctor about the risks of taking methotrexate for your condition.
The red emphasis is mine, of course. That quote comes from this National Institutes of Health site:
http://www.nlm.nih.gov/medlineplus/drug ... 82019.html
With your medical background, you're probably already familiar with methotrexate, but if you would like to see a refresher course on the risks involved with using it, that site covers it pretty well.
People who use meds such as methotrexate usually eventually discover that it no longer works from them, and they have more problems than when they started using it, and nothing provides any relief for them, any more. One of my old high school classmates is in that situation now, due to treatment for RA, and there are many, many more, all over the world. Years ago, I did my best to try to convince her and her family to try cutting gluten out of her diet, to see if that would allow her to discontinue using the Remicade, methotrexate, etc., but they refused to even try, and insisted that her doctors knew what they were doing. Now she can't even get out of her wheelchair without help, and none of the meds provide any relief anymore. We certainly don't want that to happen to you.
Tex