Atlas-based analysis is one of many analytical methods and is used to investigate typical as well as abnormal neurodevelopment. It has been widely applied to the adult and pediatric populations. Successful applications of atlas-based analysis (ABA) in those cohorts have motivated the creation of a neonatal atlas and parcellation map. The purpose of this review is to discuss the various neonatal diffusion tensor imaging (DTI) atlases that are available for use in ABA, examine how such atlases are constructed, review their applications, and observe future directions in DTI. Neonatal DTI atlases are created from a template, which can be study-specific or standardized, and merged with the corresponding parcellation map. Study-specific templates can retain higher image registration accuracy, but are usually not applicable across different studies. However, standardized templates can be used to make comparisons among various studies, but may not accurately reflect the anatomies of the study population. Methods such as volume-based template estimation are being developed to overcome these limitations. The applications for ABA, including atlas-based image quantification and atlas-based connectivity analysis, vary from quantifying neurodevelopmental progress to analyzing population differences in groups of neonates. ABA can also be applied to detect pathology related to prematurity at birth or exposure to toxic substances. Future directions for this method include research designed to increase the accuracy of the image parcellation. Methods such as multi-atlas label fusion and multi-modal analysis applied to neonatal DTI currently comprise an active field of research. Moreover, ABA can be used in high-throughput analysis to efficiently process medical images and to assess longitudinal brain changes. Nevertheless, the overarching goal of neonatal ABA is application to the clinical setting, to assist with diagnoses, monitor disease progression, and outcome prediction.