In a computing device, a method and system for searching for matching ink words or phrases, by comparing a given search term of at least one word (and possibly alternates) with the words in a document, including recognized ink words and any possible alternates for those recognized words as returned by a recognizer. Various matching tests are possible because of the use of alternates, which also may have corresponding probability rankings that may influence the search. Searching may occur in actively edited ink documents, or the recognition results may be saved as saved search file data that can be searched independent of recognition.