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We have developed an extrinsic Fabry-Perot interferometer (EFPI) to measure displacements of microscopic, living organelles in the inner ear. The EFPI is an optical phase-shifted instrument that can be used to measure nanometer displacements. The instrument transmits a coherent light signal to the end of a single glass optical fiber where the measurement is made. As the coherent light reaches the end of the fiber, part of this incident signal is reflected off the internal face of the fiber end (reference reflection) and part is transmitted through the end of the fiber. This transmitted light travels a short distance and is reflected off the surface whose displacement is to be measured (the target). This sensing reflection then reenters the fiber where it interferes with the reference reflection. The resulting interference signal then travels up the same optical fiber to a detector, where it is converted into a voltage that can be read from an oscilloscope. When the target moves, the phase relation between reference and sensing reflections changes, and the detector receives a modulated signal proportional to the target movement. Reflections of as little as 1% at both the sensor tip and target surfaces produce good results with this system. We use the EPPI in conjunction with fine glass whiskers to measure the stiffness (force per unit deflection) of stereociliary bundles on hair cells of the inner ear. The forces generated are in the tenths of picoNewton range and the displacements are tens of nanometers. Here we describe the EFPI and its development as a method for measuring displacements of microscopic organelles in a fluid medium. We also report experiments to validate the accuracy of the EFPI output and preliminary measurements of ciliary bundle stiffness in the posterior semicircular canal.