Dual energy X-ray absorptiometry (DXA) is rapidly becoming more accessible and popular as a technique to monitor body composition, especially in athletic populations. Although studies in sedentary populations have investigated the validity of DXA assessment of body composition, few studies have examined the issues of reliability in athletic populations and most studies which involve DXA measurements of body composition provide little information on their scanning protocols. This review presents a summary of the sources of error and variability in the measurement of body composition by DXA, and develops a theoretical model of best practice to standardize the conduct and analysis of a DXA scan. Components of this protocol include standardization of subject presentation (subjects rested, overnight-fasted and in minimal clothing) and positioning on the scanning bed (centrally aligned in a standard position using custom-made positioning aids) as well as manipulation of the automatic segmentation of regional areas of the scan results. Body composition assessment implemented with such protocol ensures a high level of precision, while still being practical in an athletic setting. This ensures that any small changes in body composition are confidently detected and correctly interpreted. The reporting requirements for studies involving DXA scans of body composition include details of the DXA machine and software, subject presentation and positioning protocols, and analysis protocols.