Stopped 40mg of omeprazole 2 days ago - when do side effects stop?

Usually, clearance occurs generally in 2-4 days. Some individuals are very sensitive to certain ingredients in drugs. So your GI tract may have some lingering effects for a longer period of time. It will get better. If you haven't tried a h2 receptor antagonist e.g.,famotidine, you may want to see if it works for you. It decreases acid production in the stomach. Remember every individual is very different when it comes to medications. Some have no side-effects, some have moderate and some individuals have a lot of side-effects. Unfortunately, it's a trial-error situation. One thing you may want to consider is using the lowest dose available. Make your medical providers well aware of your sensitivities!