A pen got flushed down the toilet and I am certain that somewhere down the line (no pun intended) this is going to cause an issue with toilet paper getting clogged. We tried to reach in with our hands to see if we could feel it and tried a plunger and a snake. It is an upstairs bathroom and we have not had the best of luck with plumbing over the years. Anyone have any advice on what to do? Thanks

It's possible the pen will flow through without getting hung up somewhere. I would wait and see if a backup occurs.

I doubt it would get through the trapway of the toilet. To see if it is there, wad up some toilet paper about the usual amount you use and flush see if it clogs if not try it a second time and a third if after that it hasn't clogged verify by 1 last flush with water only, it may have gone through. I'm betting that you will see a clog and you will need a 3' toilet auger with a screw hook on the end to retrieve the pen out of the toilet. Plunging the toilet will blow the paper off the pen and it will seem to flush again but the first solids that hit that pen will clog it again.

This is not a place to save money you will do nothing with the plastic cheap junk auger except spend about $10-15 on something that doesn't work. You want a "General 3' Closet Auger" it is the one that I carry on my truck and it stays on my truck because it works! It is available from our sponsor of this forum here is a link:

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Unless it was a very short pen, it is probably caught right at the top of the trap. Remove all the water from the bowl, and then use a flashlight and small mirror to look up into the toilet. If it is there, a bent coat hanger will dislodge it and let it fall back to where you can retrieve it.