I was having this problem, without this workaroung it is very likely that you (AMD user) won't be able to compile anything with homebrew.

The thing that need to be done is:

Open /usr/local/Library/homebrew/extend/ENV.rb and search for the lines starting with set_cpu_cflags then comment with a # before or change the entire line to set_cpu_cflags "arch -i386"

This way it won't be needed to edit formula by formula of the programs you want to compile and you will be able to use homebrew.

I did a fork in homebrew (github) to help ones wanting to use it oob: https://github.com/ghostec/homebrew/tree/homebrew4amd