There is some truly awesome Joker & Harley fanfiction out there on the internet. Here, I link you to the ones I especially recommend. And if you've got your own, please let me know about it!

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JokerxHarley
This is the Joker and Harley Quinn fanfiction archive, dedicated to fanfictions that specifically focus on Joker and Harley's relationship

Your Humble Webmistress' Fanfic page
Here's my fanfiction profile at fanfiction.net I've written a couple of JokerxHarley stories myself. Go read them!

Gladrial's Fanfiction Page
Some very lovely and interesting fanfiction by the fabulous Gladrial!!

Original Sin by Killing Joker
A very intriguing and well-written Jhq story!

The Mad Puppy's Fanfiction Page
Mad Puppy has written some awesome Jhq fic, so go check it out!

Mistah J's Girl's Fanfiction Page
Dark and sexy, this fic is well worth reading!

Sno-Chan's Fanfiction Page
More great fic from the awesome Sno-Chan!