Understanding the challenges associated with conducting secondary analysis of large-scale assessment data is important for identifying the strengths and weaknesses of various statistical models, and it can lead to the improvement of this type of research. The challenges encountered in the analysis of assessment data from subpopulations may be of particular value for this purpose. To date, few studies have discussed the problems associated with the secondary analysis of large-scale assessment data. By relating the experiences of a research team that engaged in several projects involving secondary analyses of linguistic minority population data from three different large-scale assessment programs, this article aims to help readers understand the practical, conceptual, and technical/statistical challenges that can be encountered.