Mesoamerican codices are manuscripts that present traits of the Mesoamerican indigenous pictoric tradition, either in content, style, or in regards to their symbolic conventions. The unambiguous presence of Mesoamerican writing systems in some of these documents is also an important, but not defining, characteristic, for Mesoamerican codices can comprise pure pictorials, native cartographies with no traces of glyphs on them, or colonial alphabetic texts with indigenous illustrations. Perhaps the best-known examples among such documents are Aztec codices, Maya codices, and Mixtec codices, but other cultures such as the Tlaxcaltec, the Purépecha, the Otomi, the Zapotecs, and the Cuicatecs, are creators of equally relevant manuscripts. The destruction of Mesoamerican civilizations resulted in only about twenty known pre-Columbian codices surviving to modern times.

During the 19th century, the word 'codex' became popular to designate any pictorial manuscript in the Mesoamerican tradition. In reality, pre-Columbian manuscripts are, strictly speaking, not codices, since the strict librarian usage of the word denotes manuscript books made of vellum, papyrus and other materials besides paper, that have been sewn on one side. Instead, precolumbian pictorials were made in native, non-codical formats, some of these being the following:

According to Donald Robertson and John B. Glass, the first scholars to propose a comprehensive census of such documents, five categories can be discerned among them. The first is that of traditional pictorials (which we will name "traditional codexes" in this article), comprising numbers 1-599 in their catalog. The second is that of paintings and maps from the Relaciones Geográficas, a set of questionnaires elaborated by the colonial bureaucracy of the Spanish Empire during the reign of Phillip II (numbers 601-699). The third category is that of Techialoyan manuscripts, a number of late colonial manuscripts created during the 17th century with the intention to serve as legal documents for indigenous communities, which display a noticeable similarity in style and format, as well as sharing a regional origin (numbers 701-799). The fourth category is that of pictorial cathecisms, also known as Testerian cathecisms (numbers 801-899). The fifth category is that of falsified pictorials. Finally, the category of nonpictorial texts which describe pictorials is contemplated, but not used, by Robertson and Glass (numbers 1000 and up), but examples of such documents exist too.

Besides this primary classification, these documents can be further classified according to their origin, their region, and subject, Thus, in regards to their origin, manuscripts can be distinguished as pre-Columbian (like those of the Borgia group), those produced under Spanish patronage (the Codex Mendoza being a notable example), native colonial (for example, Codex Xolotl), and mixed colonial (like the Lienzo de Tlaxcala). In regards to their topic, these documents can be classified as dealing with the following topics: ritual-calendrical, historical, genealogical, cartographic, cartographic-historical, economic, ethnographic, and miscellaneous.

These manuscripts can comprise many regions: Western Mexico (mainly Michoacan), Central Mexico (Mexico City and the State of Mexico, Guerrero, Hidalgo, Morelos, Puebla, Tlaxcala and Veracruz), Oaxaca, Southeast Mexico (Chiapas and Yucatan) and Guatemala. Regional schools have been identified: the classic division in the Central Mexican region was proposed by Donald Robertson, who distinguished among them the schools of Tenochtitlan, Tlatelolco and Tezcoco.

This category comprises most pre-Columbian and colonial Mesoamerican pictorials, and is by far the best-known and studied. Individual manuscripts in this category are numerous, totalling 434 in Robertson and Glass original census, and their number keeps increasing thanks to the discovery of new native traditional codices in Mexican villages. An example of a recent addition would be the Codex Cuaxicala, a pictorial document from the 16th century currently kept by the homonymous community of Huachinango, Puebla. A list of the most representative manuscripts from this category would be the following:

Within these categories, some sub-groupings of codices that are closely related in subject or that share a common prototype exist. Among the most famous are the following:

This group comprises all the paintings and illustrations from the Relaciones Geográficas, a series of documents produced as a result of questionnaires distributed to the territories under the jurisdiction of Phillip the Second, King of Spain, during the years 1579–1585. Besides their invaluable ethnohistorical, ethnological and geographical data, the Relaciones often includes a series of paintings and maps, some considered to display elements of the native cartographical tradition.