This paper investigates the free vibration of protein microtubules (MTs) embedded in the cytoplasm by using linear and nonlinear Euler-Bernoulli beam model based on modified strain gradient theory. The protein microtubule is modeled as a simply support or clamped-clamped beam. Beside, the elastic medium surrounding of MTs is modeled with Pasternak foundation. Vibration equations are obtained by using Hamilton principle and these equations are solved according to boundary conditions. Finally the dependency of vibration frequencies on environmental conditions, MTs size, changes of temperature and material length scale parameters (size effects) is studied. By comparing the findings, it could be said that the MTs' frequency is greatly increased in the presence of cytoplasm and it is very dependent to material length scale parameters. (C) 2013 Elsevier B.V. All rights reserved.