They're all the same, it's just three different possible names for the same bike. In '87 when it was thrown together it was the EX500. The 500R name came with the redesign in '94, I believe. Rumor has it that the "Ninja" and "R" was added so EX riders could feel more like a member of the ZX#R club 
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Just for reference, overseas it's called the GPZ500. Still the same bike.
.Just for reference, overseas it's called the GPZ500. Still the same bike.
