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I have the alternating nostril airway blockage and only recently (1 year ago) had the surgery.  At the same time my tonsils were removed (as an adult), I also had the uvula, (the dangling piece of skin in the back your throat) removed.  As well the ENT doctor "drilled" my nose.  It was painful, but did cure my sleep apnea.  However, within 9 months, the nostrils blockage returned.  No way am I going to go through the pain again, but it was nice when both nostrils worked/cleared.

 

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You are utterly terrible at percentages.
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Did you ever find an answer? I have exactly the same symptoms....

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I have this same problem.. EVERYday .. and have had since I broke my nose as a teen (I'm 35 now).  I think that it may have a lot to do with it as well.  I could be wrong.  but I've broken my nose now about 4 times (I'm from Texas,.. If you dont have a broken nose,..you're not having enough fun ;) ).  But I've noticed 'that' is what REALLY has seemed to kick the 'back and forth' swelling.  and same with me.. which ever side I sleep on.. the top nostril becomes clear and the bottom becomes swollen.  ALSO, when I stand quickly, seldom, but sometimes, both nostrils will clear... for a brief moment :/

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I too suffer from this same issue.  I had septoplasty and turbinate reduction surgery (using the coblation technique) about 4 years ago.  I can breathe just fine during the day, but sleeping is a disaster for me.  I wake up with the downward nostril at 0% and the upward one at 100%.  When I roll over and everything reverses.  If I lie on my back, everything is at about 50% if I'm lucky.  I've tried pseudoephedrine, but all it does is get me all wired up.  So when you're already having trouble sleeping due to problems breathing, and then add the decongestant, well, I haven't had a good night's sleep in a long time.  Sinus rinses only give marginal relief.  Nasal sprays work wonderfully, but are addictive and have terrible rebound effects on me like they do on everyone else.  Sometimes I use it just so I can get at least one good night, knowing that they'll be hell to pay for it the next night.  Anyone use a CPAP?  I've heard that it can help.  Curious if anyone has tried it specifically for treating this issue.

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I sleep with a cpap machine and its impossible to use when im stuffed up at nite so i spray affrin to go to sleep. Doctor wants a catscan done then talk surgery.

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I'm not sure it's your nose. I have this alternating nostril condition, which I assume is a deviated septum, but it doesn't really effect my breathing or phonation unless I'm sick. However, I do have an asymmetrical soft palate and small velopharyngeal gap, which causes my voice to lack in nasal quality. That could be something you could look at.
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Ok, since there doesn't seem to be an edit/delete button, I'm gonna change a few things about my last reply. I highly doubt your problem is a deviated septum, but rather, you have a underdeveloped soft palate. I have an asymmetrical soft palate which takes more time to train the muscle. In your case, it could be that you either aren't phonating properly or you have a weak soft palate.

In true cases of velopharyngeal inadequacy which can't be solved by training, there are procedure available to lengthen the soft palate, however these procedures aren't guaranteed to work.
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I've tried many drugs for this problem. Most ordered from austrailia because you don't need scipt. The corticosteroids (nasonex) work, but are steroid, so i steer clear. Someone mentioned astelin, and that seemed to work, but had a buildup issue too i think. Then i found NasalCrom at walgreens for $18. That stuff works almost instantly and says you can use it 10 times a day if you want, i usually only need two. I am off it now for a few months and suffering. I think i'll be using it until I can find a doc worth his paycheck.... so till i die. forgive my grammar, on my phone.
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Do you have an upper root canal that had been done?
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Im having the same problem but mostly my left side is blocked...Im thinking it may have to do with my root canal since its on the same side...do you have any root canals by any chance as well on the top row of your mouth...could b a factor...
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I had the same problem. Then i realised that usage of a pillow and a bed while sleeping is making the problem more severe. Then onwards i stopped using a pillow and bed. Now since 3 months iam sleeping peacefully. Try this and if it helps 

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I have had the same issue all of my life. Its comforting to see that I'm not the only one. My blockage switches nostrils without me even realizing it. I have never been able to breathe through both nostrils at 100%. 

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What problem guys? This perfectly normal en.wikipedia.org/wiki/Nasal_cycle
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Check your house for mold
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