The bulk of the Jews that died at the hands of the Nazis came from Poland where over 3 million lived. The most common estimate that I've seen is 2.5 million dead. But also remember that the Nazis slaughtered about 1.5 million Catholic Poles as well (a part of the story that is often overlooked).
The rest of the murdered Jewish civilians came from the Ukraine, Latvia, Lithuania, Hungary, France, Italy and the Balkan States.
The Polish government tends to go by the 1939 Polish census, and they found that by their next post-war census, that their population had taken a 20% drop, with something like 3 million missing Polish Jews and 3 million missing non-Jewish Poles. The 6 million missing Poles never showed back up, they were killed in various ways but the majority died in the German camps.