Her research interests are the syntax, semantics, and morphology of natural language, and the relations among these. She works on Germanic languages and on Karuk, an indigenous language of northern California. She has published on grammatical topics like noun incorporation, definiteness marking, expletive constructions, relative clauses, copular constructions, and on the relationship between word order and communicative intent. She is co-PI on an NSF-sponsored project to build a large syntactically annotated corpus of the Karuk language, which will serve as a tool for academic research as well as community language revitalization efforts. Mikkelsen has a long-standing interest in philosophy of language and is affiliated with the department of philosophy. She serves on the editorial board of the Journal of Comparative Germanic Linguistics.