Trabecular bone can be accurately represented using image-based finite element modeling and analysis of these bone models is widely used to predict their mechanical properties. However, the choice of thresholding technique, a necessary step in converting grayscale images to finite element models which can thus significantly influence the structure of the resulting finite element model, is often overlooked. Therefore, we investigated the effects of thresholding techniques on micro-computed tomography (micro-CT) based finite element models of trabecular bone. Three types of thresholding techniques were applied to micro-CT images of trabecular bone which resulted in three unique finite element models for each specimen. Bone volume fractions and apparent moduli were predicted for each model and compared to experimental results. Our findings suggest that predictions of apparent properties agree well with experimental measurements regardless of the choice of thresholding technique in micro CT images of trabecular bone.