Microimaging based finite element analysis is widely used to predict the mechanical properties of trabecular bone. The choice of thresholding technique, a necessary step in converting grayscale images to finite element models, can significantly influence the predicted bone volume fraction and mechanical properties. Therefore, we investigated the effects of thresholding techniques on microcomputed tomography (micro-CT) based finite element models of trabecular bone. Three types of thresholding techniques were applied to 16-bit micro-CT images of trabecular bone to create three different models per specimen. Bone volume fractions and apparent moduli were predicted and compared to experimental results. In addition, trabecular tissue mechanical parameters and morphological parameters were compared among different models. Our findings suggest that predictions of apparent mechanical properties and structural properties agree well with experimental measurements regardless of the choice of thresholding methods or the format of micro-CT images.