Internal reconstruction is a method of recovering information about a language's past from the characteristics of the language at a later date.
Whereas the comparative method compares variations between languages, such as in sets of cognates, under the assumption that they descend from a single proto-language, internal reconstruction compares variant forms within a single language under the assumption that they descend from a single, regular form. For example, they could take the form of allomorphs of the same morpheme. The basic premise of internal reconstruction is that a meaning-bearing element that alternates between two or more similar forms in different environments was probably a single form in the past into which alternation was introduced by the usual mechanisms of sound change and analogy.
Language forms reconstructed by means of internal reconstruction are denoted with the pre- prefix, like the use of proto- to indicate a language reconstructed by means of the comparative method, as in Proto-Indo-European. For example, internal reconstructions based on the earliest attested forms of Japanese are referred to as pre-Japanese.
It is possible even to apply internal reconstruction to proto-languages reconstructed by the comparative method. For example, performing internal reconstruction on proto-Mayan would yield pre-proto-Mayan. In some cases, it is also desirable to use internal reconstruction to uncover an earlier form of various languages and then submit those pre- languages to the comparative method. Care must be taken, however, because internal reconstruction performed on languages before applying the comparative method can remove significant evidence of the earlier state of the language and so reduce the accuracy of the reconstructed proto-language.
When undertaking a comparative study of a hitherto under analyzed family of languages it is worthwhile to get an understanding of their systems of alternations, if any, before tackling the greater complexities of analyzing entire linguistic structures. For example, Type A forms of verbs in Samoan (as in the example, below) are the citation forms, the forms in dictionaries and word lists, but when making historical comparisons with other Austronesian languages, one should not use Samoan citation forms with parts missing. (An analysis of the verb sets would alert the researcher to the certainty that many other words in Samoan have lost a final consonant.) Another way of looking at it is that internal reconstruction gives access to an earlier historical stage, at least in some details, of the languages being compared, which can be valuable: the more time that passes, the more changes accumulate in the structure of a (living) languages. Thus, the earliest known attestations of languages should be used with the comparative method.