How do I hook up my ipod to my pioneer vsx d409 ?

The best way is to use a 3,5mm stereo jack to 2 RCA cable like this:

You can easily find one like this at your local audio/electronics shop or buy one on line. You have to connect the RCA at any free stereo input at the back of your Pioneer (like aux or cd). Take a look at this picture:
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After this you can use the 3.5mm stereo jack for connecting not only your ipod but every mp3 player or other device has an earphone jack. Just plug the 3.5mm jack at the earphone jack and rise the volume at the portable device up to the middle of the volume range and set your Pioneer input selector at the stereo input that you connect the 2 RCA before (aux or cd)

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Use the earphone jack in the iPod to connect to your Pioneer's RCA analog stereo input (CD or AUX for example) using a cable with the 3.5mm plug for the iPod and the two plug RCA on the Pioneer side. Plug white into white and red into red on the Pioneer. See image below. You can buy this cable at Radio Shack or online at Amazon.com for very little. Be sure to select the Pioneer input where you connected the iPod.

Get an adapter that has ipod connection on one end, red and white auxilary jacks on the other. Hook the red and white to aux in on the back of your reciever.

You need a cable that has "mini jack" (Ipod end) to RCA stereo (receiver end). Best Buy sells them