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Why do I have a bad cough in the morning since I quit smoking?

I’m a 48 year old male, smoked since I was 16. I also have a history of sleep apnea and was hospitalized for a collapsed lung due to pneumonia. I quit smoking about two months ago. I now have a cough that wasn’t there when I smoked! Every morning when I wake up I cough so hard I’m afraid I will vomit. This goes on for about thirty minutes and then I’m ok for the rest of the day. Is this something that should pass?
Coughing in the morning can be very common in smokers due to the accumulation of toxins in the lungs, that your body then tries to cough out each morning. All of the toxins that you take in when you are smoking, in addition to causing cancer, raising your blood pressure, and ruining your teeth, also stun or kill your cilia and cause cell changes in the airway. Cilia are the small cells with microscopic brushes or fans on the edges of them, and their job is to sweep toxins and mucous out of the airway and to a point where you can cough them up. Now that you have stopped smoking (and killing them!), they are starting to work again to clean out your lungs. When you wake in the morning, you have all of the junk that was cleaned out overnight waiting to be coughed up. Despite that possible explanation, anyone with a long smoking history and a chronic cough should be seen by their doctor and probably have an x-ray to make sure that there is nothing concerning, such as lung cancer-causing the cough. Congratulations on quitting smoking, now keep taking care of yourself by seeing a physician soon to discuss your cough.
This answer is for general informational purposes only and is not a substitute for professional medical advice.
If you think you may have a medical emergency, call your doctor or (in the United States) 911 immediately. Always seek the advice of your doctor before starting or changing treatment. Medical professionals who provide responses to health-related questions are intended third party beneficiaries with certain rights under Zocdoc’s Terms of Service.

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