Within a very short period of time after you stop smoking, your lungs will begin to clear themselves out. Smoking can cause the cilia in your lungs to burn and not function properly. Cilia are tiny hairs in your respiratory system that actively move or “pump” mucous out of it in order to clear it up. If these are not functioning properly, the mucous can build up. When you quit smoking, the function of the cilia returns to normal and at the same time your body actively clears the lungs of mucous at a faster rate. As this mucous goes out of your lungs and down your esophagus, it is carrying all sorts of bacteria and irritants that may result in a sore throat. Many smokers report this as a positive feeling as they are feeling their body rid itself of all the bad stuff from their lungs despite a slightly sore throat that may result.
Another thing to note here is that because of a larger amount of mucous cleared out of your lungs, many smokers report upper respiratory infections. Your body may already be taxed by quitting smoking and the stress it can cause, adding more moisture and mucous to your system can make this an ideal setting to get a bit sick. Try eating more fruits and vegetables, along with taking a multivitamin to help prevent illness.
Part of clearing your lungs out and getting used to a non-smokers lungs will be a cough. Fortunately, this is not the same as the “smokers cough” since it is temporary and only a result of stopping smoking. Since you are no longer inhaling toxic smoke and fumes into your lungs on a regular basis, you may find that your lungs are a bit sensitive and getting used to clean air. They are also clearing themselves out so you will likely have a bit of a cough. Remember, this is part of beginning a new life and your body is adapting to a non-smokers habits.