The most common name for the confederacy, Iroquois, is of somewhat obscure origin. The first time it appears in writing is in the account of Samuel de Champlain of his journey to Tadoussac in 1603, where it occurs as "Irocois". Other spellings appearing in the earliest sources include "Erocoise", "Hiroquois", "Hyroquoise", "Irecoies", "Iriquois", "Iroquaes", "Irroquois", and "Yroquois", as the French transliterated the term into their own phonetic system. In the French spoken at the time, this would have been pronounced as [irokwe] or [irokwɛ]. Over the years, several competing theories have been proposed for this name's ultimate origin. The earliest was by the Jesuit priest Pierre François Xavier de Charlevoix, who wrote in 1744:
The name Iroquois is purely French, and is formed from the [Iroquoian-language] term Hiro or Hero, which means I have said—with which these Indians close all their addresses, as the Latins did of old with their dixi—and of Koué, which is a cry sometimes of sadness, when it is prolonged, and sometimes of joy, when it is pronounced shorter.
In 1883, Horatio Hale wrote that Charlevoix's etymology was dubious, and that "no other nation or tribe of which we have any knowledge has ever borne a name composed in this whimsical fashion". Hale suggested instead that the term came from Huron, and was cognate with Mohawk ierokwa- "they who smoke," or Cayuga iakwai- "a bear". In 1888, J.N.B. Hewitt expressed doubts that either of those words exist in the respective languages. He preferred the etymology from Montagnais irin "true, real" and ako "snake", plus the French -ois suffix. Later he revised this to Algonquin Iriⁿakhoiw.
A more modern etymology was advocated by Gordon M. Day in 1968, elaborating upon Charles Arnaud from 1880. Arnaud had claimed that the word came from Montagnais irnokué, meaning "terrible man", via the reduced form irokue. Day proposed a hypothetical Montagnais phrase irno kwédač, meaning "a man, an Iroquois", as the origin of this term. For the first element irno, Day cites cognates from other attested Montagnais dialects: irinou, iriniȣ, and ilnu; and for the second element kwédač he suggests a relation to kouetakiou, kȣetat-chiȣin, and goéṭètjg – names used by neighboring Algonquian tribes to refer to the Iroquois, Hurons, and Laurentians.
However, none of these etymologies gained widespread acceptance. By 1978 Ives Goddard could write: "No such form is attested in any Indian language as a name for any Iroquoian group, and the ultimate origin and meaning of the name are unknown."
More recently, Peter Bakker has proposed a Basque origin for "Iroquois". Basque fishermen and whalers are known to have frequented the waters of the Northeast in the 1500s, so much so that a Basque-based pidgin developed for communication with the Algonquian tribes of the region. Bakker claims that it is unlikely that "-quois" derives from a root specifically used to refer to the Iroquois, citing as evidence that several other Indian tribes of the region were known to the French by names terminating in the same element, e.g. "Armouchiquois", "Charioquois", "Excomminquois", and "Souriquois". He proposes instead that the word derives from hilokoa (via the intermediate form irokoa), from the Basque roots hil "to kill", ko (the locative genitive suffix), and a (the definite article suffix). In favor of an original form beginning with /h/, Bakker cites alternate spellings such as "hyroquois" sometimes found in documents from the period, and the fact that in the Southern dialect of Basque, the word hil is pronounced il. He also argues that the /l/ was rendered as /r/ since the former is not attested in the phonemic inventory of any language in the region (including Maliseet, which developed an /l/ later). Thus the word according to Bakker is translatable as "the killer people". It is similar to other terms used by Eastern Algonquian tribes to refer to their enemy the Iroquois, which translate as "murderers".
The Five Nations historically referred to themselves by the autonym, Haudenosaunee, meaning "People of the Longhouse". This name is occasionally preferred by scholars of Native American history, who consider the name "Iroquois" derogatory. The name derives from two phonetically similar but etymologically distinct words in the Seneca language: Hodínöhšö:ni:h, meaning "those of the extended house," and Hodínöhsö:ni:h, meaning "house builders". The name "Haudenosaunee" first appears in English in Lewis Henry Morgan (1851), where it is written as Ho-dé-no-sau-nee. The spelling "Hotinnonsionni" is also attested from later in the nineteenth century. An alternate designation, Ganonsyoni, is occasionally encountered as well, from the Mohawk kanǫhsyǫ́·ni ("the extended house"), or from a cognate expression in a related Iroquoian language; in earlier sources it is variously spelled "Kanosoni", "akwanoschioni", "Aquanuschioni", "Cannassoone", "Canossoone", "Ke-nunctioni", or "Konossioni". More transparently, the Iroquois confederacy is also often referred to simply as the Six Nations (or, for the period before the entry of the Tuscarora in 1722, the Five Nations). The word is Rotinonsionni in the Mohawk language.