The Cholesky decomposition method is the gold standard used in the field of behavioral genetics. The method is popular because it is easy to program and solve. Using this method, researchers can explore individual differences in longitudinal relations of different variables across multiple time points. The method allows investigators to decompose variance into (1) unique genetic, shared and non-shared environmental effects that arise at specific time points as well as (2) overlapping genetic, shared and non-shared environmental effects that carry over from one time point to another. However, the method does not identify the mechanisms or origins underlying these effects. The current report focuses on application of the Cholesky decomposition method in the field of educational psychology. Specifically, it discusses individual differences in longitudinal relations between kindergarten letter knowledge, kindergarten phonological awareness, first grade word-level reading skills, and seventh grade reading comprehension.