In the 1850s, Haldeman's focus turned to the study of language. He carried out extensive research among Amerindian dialects, and also in Pennsylvania Dutch, besides investigations in the English, Chinese, and other languages. Haldeman was an earnest advocate of spelling reform. He was a member of many scientific societies, was the founder and president of the American Philological Association, and one of the early members of the National Academy of Sciences. In 1858, Haldeman was awarded the Trevelyan Prize, given by the Phonetic Society of Great Britain, for his article entitled "Analytic Orthography". He made numerous visits to Europe for purposes of research, and when studying the human voice in Rome determined the vocal repertoire of 40–50 varieties of human speech. In 1869, he returned to the University of Pennsylvania as a professor of comparative philology and remained there until his death in 1880.
