This is also the reason why it is called AMD64. Intel for its 64-bit lineup had bet on it's Itanium lineup of processors which included a completely new 64-bit instruction set which was not backwards compatible with Intel's 32-bit x86 instruction set.
AMD when releasing the spec called it AMD64 (FreeBSD, Debian, *BSD), and the name stuck for certain projects, other names are x86_64 (Apple), x64 (Sun/Oracle, Microsoft). There are a variety of ways to refer to the instruction set, but what is sure is that AMD was the first to market with it, so saying AMD64 is code name for the popular Intel 64-bit architecture is not entirely correct. Intel 64 is a code name for AMD64, AMD's 64 bit extensions to Intel's 32-bit x86 architecture.
It should not be confused with "IA64", aka the "Intel Itanium 64" architecture, which was Intel's mostly-dud non-x86 compatible attempt at 64 bit architecture, a clean break from the x86 legacy. http://en.wikipedia.org/wiki/Ia64#Architecture