Hi.. Thanks for the query.. I have gone through your query and can understand your concern. As per your complain and presentation of symptoms a blood clot in mouth can be most commonly due to gum bleeding if there is infection in gums causing inflammation. The chances of blood in mouth on waking up increases if along with gum inflammation there is also mouth breathing habit and continuous in and out of air leads to dryness and irritation in gums causing bleeding.. Nothing to worry about it, consult an oral physician and get evaluated and if there is gum inflammation Scaling followed by a short course of antibiotics and topical application of gum paint will relieve.. If you have mouth breathing habit a simple remedy will help. You can stick a vertical strip of micropore tape or doctor s tape over your closed lips as it will enforce nasal breathing as well as prevent bleeding from gums and also dryness in mouth.. Hope this information helps.. Thanks and regards.. Dr.Honey Nandwani Arora.