The locomotion of many bacteria and millimetre-sized ciliates includes stochastic reorientation steps. Appendages such as cilia or flagella can be deployed to exert a resisting or propelling force which can affect the reorientation. Whether this characteristic enables ciliates to control their tumbling velocity is debatable. This problem can be formalized by means of a fluid-structure interaction model in the steady Stokes regime [1]. We propose a two-way coupled fluid-structure interaction model to describe the kinematics of a ciliated microorganism subjected to a general Stokes flow. Each cilium is modelled as a rigid rod connected to the body with a cylindrical joint. The force exchanged by the cilia and the fluid is represented by means of the Johnson’s slender body theory [2]. The resulting model offers meaningful insights about the reorientation of ciliates in linear flows.