We describe a new counter-rotating Couette apparatus that has been developed for deformation studies of single sub-millimeter sized particles in shear flow. New features are the adaption to the low viscosities of water-based systems and temperature control of the device. The inner to outer radius ratio of the cylinders used is 0.9785 and the height to width aspect ratio of the gap is 4.0, while the inner radius is 100 mm. Because of the limited particle size a high mechanical accuracy of the Couette geometry is necessary. The swing of the inner cylinder is less than 2 μm and that of the outer cylinder less than 4 μm. We achieved this by carefully choosing the design parameters of the aerostatic bearing and the coupling between cylinder and motor unit. Furthermore, special drive units give a shear rate resolution of 0.018 s−1, while the maximum shear rate is 100 s−1. For a liquid viscosity on the order of 1 mPas the effective maximum shear rate is 30 s−1. We have shown that deformations as small as (L−B)/(L+B) ≈ 0.01 of giant bilayer vesicles (typical radius 10 μm) with length L and width B can be observed with our device.