Abstract In this paper, mechanical responses of isolated microtubules are investigated. Microtubules can be defined as bio-composite structures that are a component of the cytoskeleton in eukaryotic cells and play important roles in cellular processes. They have superior mechanical properties such as high rigidity and flexibility. In order to model the microtubules such as a hollow beam, a trigonometric shear deformation beam model is employed on the basis of modified strain gradient theory. The governing equations and related boundary conditions are derived by implementing Hamilton’s principle. A detailed parametric study is performed to investigate the influences of shear deformation, material length scale parameter-to-outer radius ratio, aspect ratio and shear modulus ratio on mechanical responses of microtubules. It is observed that microstructure-dependent behavior is more considerable when material length scale parameters are closer to the outer diameter of microtubules. Also, it can be stated that effects of shear deformation become more significant for smaller shear modulus and aspect ratios.