It also caused a little bit of controversy for its use of religion, so much so that a proposed 3DS edition was scuppered by Nintendo itself.
However, creator Edmund McMillen has revealed that there could be a chance for an updated version of the game to appear on Nintendo's popular handheld - although at the moment, he thinks its only 50/50.
Speaking more about the remake, he had this to say:
The remake will be more than just an expansion, it will be a new game with all new graphics, music, etc. It will also feature an expansion-sized pack of all new content, bosses, characters enemies, items etc. And yes, in about a year if/when it comes out, the Flash version of the game will appear obsolete for sure. But a year is a long time and I'll do what I can to make sure the guys who remake it make it substantial enough for you to play through all over again.
Fingers firmly crossed, then - despite the fuss surrounding its subject matter, The Binding of Isaac has received positive reviews from many quarters.