Hello - This could be caused by Anxiety believe it or not. Since you said the X-ray was clean, perhaps he has insomnia (and has not told you about it) which in turn, can cause anxiety at night, causing the symptoms you mentioned. It is not uncommon to feel like you are even having a HEART ATTACK during Anxiety attacks (minor and major) - If it only occurs at NIGHT when he is lying down, it sounds like the stress of lying down is causing him to panic (Anxiety is REAL, it is not a made up thing in your head ) it can cause a lot of problems and people don t even realize they are having a panic/anxiety attack. Now, on the otherhand, he could have a minor infection that an X-Ray would not show. You could ask for a Sputum test (testing of the mucus) to see if when he coughs, he coughs mucus - Then have it tested for bacterias and/or other infections. However (without sounding like I am dismissing this, as I too am a victim of Anxiety) IT SOUNDS LIKE ANXIETY. Only at night, he is fine all the other times...No coughing, no pain, nothing...Only at night, bedtimes, alone...THOUGHTS in his head...SCHOOL...HOMEWORK. I was in Afghanistan in the US ARMY and had PTSD back in 2007, I suffer from Anxiety and Panic from time to time, and it happened most when it was time to go to bed, as that is the time when the mind RESTS but RUNS WITH THOUGHTS. I hope this helps - However, I would recomend the Sputum test if he does cough and show other signs of infection, like fever, or redness, or ichyness.