The main purpose of this paper is to demonstrate how to apply the Hierarchical Linear Modeling (HLM) technique to multi-wave Curriculum-Based Measurement (CBM) measures in modeling academic growth and assessing its relations to student-and instruction-related variables. HLM has advantages over other statistical methods (e.g., repeated measures ANOVA, Structural Equation Modeling) in modeling academic growth. The advantages include allowing more flexible research designs in collecting multiple data points and estimating growth rates and their relations to correlates in more reliable, accurate ways. CBM, as a multi-wave progress-monitoring system, also has distinctive psychometric features that facilitate longitudinal research on academic skill development. These features include provision of multiple data points within short time periods, good validity and reliability, and sensitivity for detecting small degrees of change. Finally, research questions related to assessing the academic growth of students with learning difficulties and using assessment results to improve educational practices for them are discussed.