Background and Objective: In epidemiological research, studying the long-term dependencies between multiple diseases is important. This study extends the multilevel Bayesian network (MBN) for repeated measures data that can estimate the rate of change in outcomes over time while quantifying the variabilities of these rates across higher-level units through various variance-covariance structures., Method: The performance and reliability of a model are examined through a simulation study, and its practical application is demonstrated using child morbidity data. This data has a hierarchical structure in which children were randomly selected from clusters (villages) and their conditions were assessed quarterly from March 2015 to May 2016. MBN was used to explore the relationship between outcomes weight-for-age (WAZ), height-for-age (HAZ), the number of days a child suffers from diarrhea (NOD), and flu (NOF), and estimate the rate of change of these outcomes over time. Since the outcomes considered were hybrid in nature, the connected three-parent set block Gibbs sampler with a multilevel generalized Poisson regression, multilevel zero inflated Poisson regression, and linear mixed-effects models were considered during the structure and parametric learning of the MBN., Result: The simulation study confirmed that a MBN using the time metric t as a node performed well for repeated measures data. The result from the structure learning of MBN shows a causal relationship between WAZ, HAZ, NOD and NOF. Furthermore, exclusive breastfeeding months and usage of micronutrient powder appeared as a strong predictor for all outcomes considered in this study., Conclusion: This study reveals that MBN is suitable in modeling repeated measures data to study the relationship between outcomes and estimate rate of change of an outcome over time while quantifying the variability due to higher-level clustering variables. Furthermore, the study highlights the importance of focusing on monitoring children with low WAZ and HAZ scores together with good feeding practices against the frequency of getting flu and diarrhea., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)