The side effects of probiotics are usually minor. Most people (including myself) do not experience any unpleasant reaction at all when they start a course of probiotics.
A few people suffer a herx reaction which is when you feel worse after starting something than you did before you started.
It happens when large quantities of toxins are dumped into the body as bacteria die and commonly happens in the early stages of many healing reactions including healing yourself with probiotics.
So you might find you have bloating, wind, or diarrhea and even flu-like symptoms such as fever, chills, muscle pain and headaches, or a worsening of allergies.
The herx reaction normally last for only a few days.
Ease off the amount of the probiotic you are taking, whether it is a supplement or a food source such as yogurt and once the probiotics side effects have lessened, gradually increase the amount again.
Some bacteria in our intestinal tract digest the fiber from our food producing gases such as methane and hydrogen as an end product. Other bacteria absorb these gases for their own metabolic processes.
As soon as you alter your diet in any way, either by making different food choices or by taking supplements then it is possible for these two different types of bacteria to get out of balance. If you end up with more gas producers than gas absorbers then the passing of wind (flatulence) is usual. This is one of the most common side effects of probiotics.
Interestingly, it is often the prebiotics - the dietary fiber that is added to some probiotics - that is the cause of that feeling of urgency and wind.
Prebiotics such as FOS (fructo-oligosaccaride) are fermented in the colon rather than digested in the small intestine which is where food is more normally digested. Therefore all the usual effects of intestinal gas such as distention of the bowel, pain and the passing of wind can be caused.
As prebiotics are being added to more and more probiotics, so manufacturers are looking at sources of dietary fiber that product the least amount of gas production. That's one side effect of probiotics that you don't need.