An extension of the latent Markov Rasch model is described for the analysis of binary longitudinal data with covariates when subjects are collected in clusters, such as students clustered in classes. For each subject, a latent process is used to represent the characteristic of interest (e.g., ability) conditional on the effect of the cluster to which he or she belongs. The latter effect is modeled by a discrete latent variable associated to each cluster. For the maximum likelihood estimation of the model parameters, an Expectation-Maximization algorithm is outlined. Through the analysis of a data set collected in the Lombardy Region (Italy), it is shown how the proposed model may be used for assessing the development of cognitive achievement. The data set is based on test scores in mathematics observed over 3 years on middle school students attending public and non-state schools. (Contains 13 tables and 2 figures.)