The orientation and configuration of the central-pair microtubules in cilia were studied by serial thin-section analysis of "instantaneously fixed" paramecia. Cilia were frozen in various positions in metachronal waves by such a fixation. The spatial sequence of these positions across the wave represents the temporal sequence of the positions during the active beat cycle of a cilium. Systematic shifts of central-pair orientation across the wave indicate that the central pair rotates 360 degrees counterclockwise (viewed from outside) with each ciliary beat cycle (C. K. Omoto, 1979, Thesis, University of Wisconsin, Madison; C. K. Omoto and C. Kung, 1979, Nature [Lond.] 279:532-534). This is true even for paramecia with different directions of effective stroke as in forward- or backward-swimming cells. The systematic shifts of central-pair orientation cannot be seen in Ni++-paralyzed cells or sluggish mutants which do not have metachronal waves. Both serial thin-section and thick-section high-voltage electron microscopy show that whenever a twist in the central pair is seen, it is always left-handed. This twist is consistent with the hypothesis that the central pair continuously rotates counterclockwise with the rotation originating at the base of the cilium. That the rotation of the central pair is most likely with respect to the peripheral tubules as well as the cell surface is discussed. These results are incorporated into a model in which the central-pair complex is a component in the regulation of the mechanism needed for three-dimensional ciliary movement.