Accidental nasopharyngeal colonization of a laboratory worker by a human disease isolate of Neisseria meningitidis allowed us to examine the variation in expression of outer membrane components and the host humoral response over time. There were quantitative differences in class 1 outer membrane protein expression in nasopharyngeal isolates obtained at different times. Isolates also showed phase variation of all four class 5 outer membrane proteins produced by the colonizing strain. After colonization, we detected new host serum immunoglobulin G antibodies directed against class 1, class 5, and H.8 outer membrane proteins.