When he traveled to the Southwest United States with the Hemenway expedition, he used a phonograph to record music of the Zuni (1890) and Hopi (1891).

Benjamin Ives Gilman used these recordings to show that the people used musical intervals unlike those in the Western tempered scale.

He particularly focused on the variants and styles of prehistoric Southwest Indian pottery, producing a number of volumes with carefully drawn illustrations.

If this destruction of the cliff-houses of New Mexico, Colorado, and Arizona goes on at the same rate in the next fifty years that it has in the past, these unique dwellings will be practically destroyed, and unless laws are enacted, either by states or by the general government, for their protection, at the close of the twentieth century many of the most interesting monuments of the prehistoric peoples of our Southwest will be little more than mounds of debris at the bases of the cliffs.

A commercial spirit is leading to careless excavations for objects to sell, and walls are ruthlessly overthrown, buildings torn down in hope of a few dollars' gain.

Students who follow us, when these cliff-houses have all disappeared and their instructive objects scattered by greed of traders, will wonder at our indifference and designate our negligence by its proper name.

It would be wise legislation to prevent this vandalism as much as possible and good science to put all excavation of ruins in trained hands.His research on pre-Columbian sites in Puerto Rico, Haiti, Cuba, Trinidad, and the Lesser Antilles was the basis for his 1907 book, Aborigines of Porto Rico and Neighboring Islands, an acclaimed book in early archaeology.