A third of new drugs approved by the FDA in recent years and then prescribed by doctors to their patients have later been found to cause major side effects that were not initially detected. The average time of these major health issues caused by these new medications (which include severe allergic reactions, liver damage, cancer, or death) is about four years. As a physician, I never prescribe a new drug (unless for a life threatening condition where no other options are available) until several years have passed and much more clinical information has been gathered.
Before the FDA approves a new drug, in most cases, the studies include fewer that 1,000 test subjects and a period of use less than 6 months. In the real world millions of people may eventually take the drug regularly and for much longer periods, thus unmasking adverse reactions that were not initially noticed with a smaller sample of users and for shorter periods of use. This is true also for some herbal supplements, which, although inherently much safer, have often not been studied for prolonged periods. That is why I often recommend people not take the same supplement for long periods without breaks.
Before you fill out a new medication prescribed to you by your doctor, ask how long it has been on the market and how much experience your doctor with it and feedback that he or she has had from patients using it.