The Chlamydia trachomatis inclusion is fragile, rendering it incompatible to micromanipulation. We show that the Chlamydia pneumoniae inclusion differs, being resistant to micromanipulation as shown by direct microinjection of the infected host cytosol or the inclusion itself. We have used micromanipulation to clone C pneumoniae and to free it from mycoplasma contamination. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.