After we flush either of our toilet upstairs we can hear it going through the pipe in the ceiling. I believe it was happening when we first moved in (5 years ago)and it went away on it's own. Any idea what it is? Is this something that we should have checked out or is there a way we can stop it on our own?

It is not uncommon for you to be able to hear a toilet flushing, especially if the drain is PVC. A csat iron pipe tend to deaden the sound. It is unusually for the sound to come and go. Has then been any insulation or remodeling done lately?

Nope, no remodeling has been done. Is it something I should have checked out?

Are your drain pipes PVC? If you aren't sure look in the basement and see what color the pipe is as it exits the house. White or pale green are plastic and they tend to make more noise.

Unfortunately if it is in the ceiling, there is little option. The only way to reduce water noise is to insulate the pipe and that would require opening the ceiling. Sorry.