It does not seem to negatively effect medications in most cases. And many people find they can lower medication doses, as their body functions improve. This is especially true of joint and migraine pain medications, allergy medications etc. (MSM helps treat those issues)
Of course do discuss your specifics with your Dr or Pharmacist to confirm that it will not present an issue for your health and medication concerns, as I am not a qualified medical professional.
Side effects are temporary, related to the detox issues when you first use it, or first up your doses. It is less toxic then water.
The link I posted above on the De-Tox is a good read about that. Also review the messageboard link I posted for more details, on possible issues with different health concerns or meds. You may need to adjust your dose for your specific situation. You can also email Kerry on the MSM-MSM.com site. (hes the owner, posts on the board, and you can reach him through the Contact link) He is very friendly, knowledgeable and very very helpful.
If you have a damaged or weak liver or kidney issues, do take small doses and move up very slowly so as not to overwhelm your waste removal system with to many toxins at once.
MSM does not build up in the body, it flushes out with your urine, with a half life of 12 hours. Which is why you should take a dose every 12 hours to keep levels high. A compromised waste removal system can change this timeframe.
Many take amounts as high as 50,000 mg or more, for disease treatments, without side effects. (I don’t recommend that level unless under a Dr care of course)