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Hmmm I used to have that same problem when I used my aux cord. I also have a pioneer stereo in my honda prelude. Instead of using your aux output i would recommend using USB if your stereo has it. I plug in my Iphone via USB and the audio is crystal clear. Plus the cord is alot more durable than aux cords. Every aux cord ive ever owned lasted less than a month due to my friends twisting and pulling on it, when their tryin to play their music from my backseat! Lol it pissed me off when people get in my car and think they can control my music the whole time.

[quote="wulfman"]I have a Pioneer system in my MDX. It works great with the radio and CDs, but when I have my phone plugged into the auxiliary input, the sound only comes out of the right side. Its not the phone because I've tested other devices. Also replaced the cable.
I have to use a cable and I was told that is the problem but I've tried everything. My radio has no USB input or blue tooth.[/quote]

If you've already replaced the cable, and also tried other devices. Sounds like there is something wrong with the input for the AUX.
Just to confirm, have you tried using that cable on another device, just to rule it out?

I have a Pioneer system in my MDX. It works great with the radio and CDs, but when I have my phone plugged into the auxiliary input, the sound only comes out of the right side. Its not the phone because I've tested other devices. Also replaced the cable.
I have to use a cable and I was told that is the problem but I've tried everything. My radio has no USB input or blue tooth.