Quantitative CT (QCT) analysis involves the calculation of specific parameters such as bone volume and density from CT image data, and can be a powerful tool for understanding bone quality and quantity. However, without careful attention to detail during all steps of the acquisition and analysis process, data can be of poor- to unusable-quality. Good quality QCT for research requires meticulous attention to detail and standardization of all aspects of data collection and analysis to a degree that is uncommon in a clinical setting. Here, we review the literature to summarize practical and technical considerations for obtaining high quality QCT data, and provide examples of how each recommendation affects calculated variables. We also provide an overview of the QCT analysis technique to illustrate additional opportunities to improve data reproducibility and reliability. Key recommendations include: standardizing the scanner and data acquisition settings, minimizing image artifacts, selecting an appropriate reconstruction algorithm, and maximizing repeatability and objectivity during QCT analysis. The goal of the recommendations is to reduce potential sources of error throughout the analysis, from scan acquisition to the interpretation of results.