In this study, we investigate how morphological parameters and mechanical properties derived from microcomputed tomography (μCT) are affected by small errors in threshold value when variable bone structures and different bone volume fractions are involved. For this purpose, biopsies of vertebrae of 6-, 23-, and 230-week-old female pigs were scanned using μCT. For each specimen, five threshold values were determined within the range of thresholds that an observer could select realistically, in steps of 0.5%. The scans were converted to microfinite-element (μFE) models, used to determine the elastic moduli. A variation of 0.5% in threshold resulted in a 5% difference in bone volume fraction and 9% difference in maximal stiffness for bone cubes with a volume fraction of <0.15. When the volume fraction was >0.2, these differences were only 2% and 3%, respectively. For all bone cubes, the differences for trabecular thickness and bone surface density were <3%. The effects on morphological anisotropy and trabecular number were negligible for threshold variations of 0.5%. These findings suggest that threshold selection is important for the accurate determination of volume fraction and mechanical properties, especially for low bone volume fractions;​ the architectural directionality is less sensitive to changes in threshold.