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Here's the researchers' studied estimate based on years of going through and double checking the names and death reports - although not complete at that point, I believe the number is officially still lower than their roof estimate total. The civilian break down is as follows, which is still a large death toll but less than 1/6 the 250,000 Muslim civilians figure bandied about.

“The researchers estimate the number of killed civilian Muslims and Croats to be around 38,000, while the number of killed civilian Serbians was about 16,700.”

http://www.freerepublic.com/focus/f-news/1291965/posts

So the total for BOTH Muslim and Croat civilians is 38,000. Those groups had their own intense war between each other (late 1992 until a U.S. brokered peacedeal ended their fighting in late Feb. 1994) separate from the main war they had against the Serbs - this took place where Serb forces were gone and most, if not all Serb civilians too.

The numbers of Croat and Muslim civilians killed during the Muslim-Croat war within the general Bosnian war is not separated out of the general total. There were also a lot of foreign mercenaries who were going around killing Bosnian civilians of all ethnicities. The foreign mercenaries including many from Germany and Britain (non-Muslims who fought for the Muslim or Croats) in addition to thousands of Muslims from the Middle East, Africa, Europe, etc.

The Mujahadeen were based in Central Bosnia where there were many Croats. A Scottish mercenary, John MacPhee, fighting for the Croats was witness to (and wrote a book on the mayhem these Muslims did on Bosnian Croat civilians, including babies and children.