Morton published an important collection of illustrations delineating pulmonary tuberculosis which epitomized the knowledge of his time. It was also the first book on the subject published in the United States. Digital facsimile from the National Library of Medicine, Internet Archive at this link.

In his day Morton was the most eminent craniologist in the United States. He had a collection of nearly 1,000 skulls. In this work, which described both modern and fossil skulls, Morton described fractures and anthropogenic deformations. Digital facsimile from the Internet Archive at this link.

Numbers 901-929 in Morton's catalogue are "Thirty Skulls of genuine unmixed NEGROES born in Africa. This interesting series series was collected by Don José Rodriguez Cisnerso, M. D. of Havana, in the island of Cuba, and by him presented to me for the purpose of ascertaining the internal capacity of the cranium in the pure AFRICAN race."

Morton believed that he could define the intellectual ability of a race by the skull capacity. A large volume meant a large brain and high intellectual capacity, and a small skull indicated a small brain and decreased intellectual capacity. He also claimed that each race had a separate origin, and that a descending order of intelligence could be discerned that placed Caucasians at the pinnacle and Negroes at the lowest point, with various other races in between. Considered the origin of scientific racism, this theory provided a "scientific" justification for slavery.

 "Samuel George Morton is often thought of as the originator of "American School" of ethnography, a school of thought in antebellum American science that claimed the difference between humans was one of species rather than variety and is seen by some as the origin of scientific racism.^[6]

"Morton argued against the single creation story of the Bible (monogenism) and instead supported a theory of multiple racial creations (polygenism). Morton claimed the Bible supported polygenism, and within working in a biblical framework his theory held that each race had been created separately and each was given specific, irrevocable characteristics.^[7]

"After inspecting three mummies from ancient Egyptian catacombs, Morton concluded that Caucasians and Negroes were already distinct three thousand years ago. Since the Bible indicated that Noah's Ark had washed up on Mount Ararat, only a thousand years ago before this, Morton claimed that Noah's sons could not possibly account for every race on earth. According to Morton's theory of polygenesis, races have been separate since the start^{[7] " (Wikipedia article on Samuel George Morton, accessed 01-2017).}

Digital facsimile of the 1840 edition from the Internet Archive at this link. Morton continued to develop and expand his collection, which reached 1512 human and animal skulls in the third edition of his catalogue published in 1849. That catalogue contained an introduction, some illustrations, and a complete index. Digital facsimile of the 1849 edition from the Internet Archive at this link.

Morton's last paper on the measurement of cranial capacity and its relationship to intellectual ability may have been "Observations on the size of brain in various races and families of man," Proceedings of the Academy of Natural Sciences, October, 1849.  Digital facsimile from the Internet Archive at this link.

Morton argued that blacks and whites had been racially distinct since the Egyptian First Dynasty and drew the following conclusions, long since debunked:

"Conclusions.

"1. The valley of the Nile, both in Egypt and in Nubia, was originally peopled by a branch of the Caucasian race.

"2. These primeval people, since called Egyptians, were the Mizairmites of Scripture, the poster ity of Ham, and directly affiliated with the Libyan family of nations.

"3. In their physical character the Egyptians were intermediate between the indo-European and Semitic races.

..."8. Negroes were numerous in Egypt, but their social position in ancient times was the same as it now is, that of servants and slaves" (pp. 65-66).

Nott, a prominent physician and anthropologist in Mobile, Alabama, employed polygenist arguments to justify slavery. This required resoilving the problem of racial hybridity. Polygenists claimed that different races were different species. Species, however, were supposed to be incapable of producing fertile offspring, while it was obvious that different races, specifically white and black could reproduce and create mulattoes. To keep the designation of races as 'species' intact, Nott redefined the definition of species, making its essential characteristic not hybrid infertility, but morphological distinctness through time-time longer than could be inferred from the Bible. . . . Nott sought to disassociate anthropology from the Bible. His alternative explanation was that races had been separately created before Biblical time. His medical experience convinced him that blacks and whites possessed different susceptibilities to disease, attributable to innately different 'vitalities.' Nott argued against monogenist anthropologists, who believed that races had a recent and common origin. . . .Nott's comments on race brought him to the attention of other members of the American School, including its proclaimed leader, Samuel George Morton. After Morton's death, George Glidden, then the U.S. consul in Cairo, persuaded Nott to co-author a book, Types of mankind, dedicated to Morton's memory. Gliddon's contribution was to show that blacks and whites had been distinct as early as Egypt's first dynasty. Nott's contribution was also intended to demonstrate the antiquity of racial differences, as well as to show that races were immune to major change. Digital facsimile of the 1854 second edition from the Internet Archive at this link. Sttee Paul A. Erickson, The anthropology of Josiah Clark Nott avaiable from digitalassets.lib.berkeley.edu at this link.

"Since the death of the late lamented President of the Academy of Natural Sciences,- Dr. Samuel George Morton,- his magnifcent Collection of Human Crania, recently increased by the receipt of 67 skulls from various sources, has been permanently deposited in the Museum of the Academy. Prior to his demise, Dr. M. had recieved 100 crania in addition to those mentioned in the third edition of his Catalogue. Since 1849, therefore, the Collection has been augmented by the addition of 167 skulls. To complete the Catalogue in a uniform manner, these have been carefully numbered and measured in accordance with the methods recorded in the Crania Americana, &c....

"The entire Collection,- numbering 1035 crania,- was purchased by forty-two gentlemen from the executors of Dr. Morton, for the sum of $4,000 and by them generously presented to the academy.

"The Collection occupies 16 cases on the first gallery, on the south side of the lower room of the Museum. For convenience of study and examination I have grouped the crania according to Race, Family, Tribe, &c., strictly adhering, however, to the classification of Dr. Morton....(p, 3).

"Extensive and unique as is the Collection, it is, nevertheless, still too limited to justify positive and comprehensive conclusions concerning the great fundamental problems of Ethnology. That it will be capable, when sufficiently extended, of throwing much light upon these obscure and unsettled questions is amply attested by the scientific publications of Dr. Morton. It is earnestly hoped, therefore, that this magnificent nucleus, the result of much pecuniary sacrifice and many years of enthusiastic labor on the part of its late illustrious owner and founder, will not be neglected, but that its efficiency will be increased, and the objects for which it was gathered together attained by contributions from all who may be interested in the advancement of this youngest, most intricate, and most important of the sciences" (p. 11). Digital facsimile from Google Books at this link.