Does smoking cigarettes affect the digestive system? Not in the commonly known laxative way, but does it interfere with digesting food, absorbing nutrients and the effectivness of the digestive system? I have been trying to work out if I have a food intolerance, but now I think its smoking. I smoked 10 cigarettes a day for 15 years, but over the last few months Ive cut down to just 10 on the weekend, and my digestive system has gone to pot. My diet hasn't really changed.