Are there side effects of taking omega 3s? Sue Brennan: Primarily, side effects that have been reported, have been gastrointestinal. You can have a fishy taste in your mouth after taking them. That’s common. If people start with too big of a dose, they might end up with some diarrhea. So, my advice is to chose a good quality product because that can help minimize some of that taste problem. Also, to start your dose lower and gradually work up to avoid any diarrhea problems. Taking with a meal, taking with food can also minimize the stomach effects. Skin rash has been reported but that’s fairly rare—but it’s something that if you do get a rash, overall body rash following, you know, starting the omega 3s, you should let your doctor know.