When Civil War History published a paper this spring raising the conflict’s military death toll to 750,000 from 620,000, that journal’s editors called it one of the most important pieces of scholarship ever to appear in its pages.

But to Jim Downs, an assistant professor of history at Connecticut College and the author of the new book “Sick From Freedom,” issued last month by Oxford University Press, that accounting of what he calls “the largest biological crisis of the 19th century” does not go nearly far enough.

To understand the war’s scale and impact truly, Professor Downs argues, historians have to look beyond military casualties and consider the public health crisis that faced the newly liberated slaves, who sickened and died in huge numbers in the years following Lincoln’s 1863 Emancipation Proclamation.

“We’re getting ready to celebrate 150 years of the movement from slavery to freedom,” he said in a recent interview at a cafe near his apartment in Chelsea. “But hundreds of thousands of people did not survive that movement.”...