I have a 2008 Honda civic with 64000 miles. Recently I have been hearing a rattling noise coming from the rear passenger side of the vehicle when driving over bumps or rough roads. I thought the noise was coming from something moving around in the trunk but I removed everything and the noise is still there. when the noise first started, I would rarely hear it. Now i hear it all the time.

 

Many rattles under a car are exhaust system related. You could try grabbing the muffler and/or tailpipe and shaking to see if anything rattles.

 

I just experienced a rattling sound coming from the trunk in my 2008 Civic and found that dirt/debris had accumulated between the underside of the trunk/floor and a plastic shield. Seems that dirt was kicked in by the rear passenger tire. I banged out the dirt and the sound seems gone.