In this paper, vibration of the protein microtubule, one of the most important intracellular elements serving as one of the common components among nanotechnology, biotechnology and mechanics, is investigated using stress and strain gradient elasticity theory and orthotropic elastic shells model. Microtubules in the cell are influenced by internal and external stimulation and play a part in conveying protein substances and taking medications to the intended targets. Therefore, in order to control the biological cell functions, it is important to know the vibrational behavior of microtubules. For this purpose, using the cylindrical shell model which fully corresponds to microtubule geometry, and by considering it as orthotropic which is closer to reality, based on gradient elasticity theory, frequency analysis of the protein microtubule is carried out by considering Love’s thin shell theory and Navier solution. Also, the effect of size parameter and other variables on the results are investigated.