Two morphological characteristics of the Malayo-Polynesian languages are a system of affixation and the reduplication (repetition of all or part of a word, such as wiki-wiki) to form new words. Like other Austronesian languages they have small phonemic inventories; thus a text has few but frequent sounds. The majority also lack consonant clusters (e.g., [str] in English). Most also have only a small set of vowels, five being a common number.
The Malayo-Polynesian languages share several phonological and lexical innovations with the eastern Formosan languages, including the leveling of proto-Austronesian *t, *C to /t/ and *n, *N to /n/, a shift of *S to /h/, and vocabulary such as *lima "five" which are not attested in other Formosan languages. However, it does not align with any one branch. A 2008 analysis of the Austronesian Basic Vocabulary Database suggests the closest connection is with Paiwan, though it only assigns that connection a 75% confidence level.
Malayo-Polynesian consists of a large number of small local language clusters, with the one exception being Oceanic, the only large group which has been reconstructed and is indisputably valid. All other large groups within Malayo-Polynesian are disputed. The family has traditionally been divided into Western ("Hesperonesian"), Central, and Eastern branches. However, there is little support for these groups; Central MP languages are distinctive because they are typologically Melanesian due to substratum effects of the Papuan languages of eastern Indonesia, as similarly are the Eastern MP languages, while the Western branch is simply the branches which have not undergone such extensive contact-induced change.