MOTIVATION: Patient stratification is crucial for the effective treatment or management of heterogeneous diseases, including cancers. Multiomic technologies facilitate molecular characterization of human diseases; however, the complexity of data warrants the need for the development of robust data integration tools for patient stratification using machine-learning approaches. RESULTS: CluF iteratively integrates three types of multiomic data (mRNA, miRNA, and DNA methylation) using pairwise patient similarity matrices built from each omic data. The intermediate omic-specific neighborhood matrices implement iterative matrix fusion and message passing among the similarity matrices to derive a final integrated matrix representing all the omics profiles of a patient, which is used to further cluster patients into subtypes. CluF outperforms other methods with significant differences in the survival profiles of 8581 patients belonging to 30 different cancers in TCGA. CluF also predicted the four intrinsic subtypes of Breast Invasive Carcinomas with adjusted rand index and Fowlkes-Mallows scores of 0.72 and 0.83, respectively. The Gini importance score showed that methylation features were the primary decisive players, followed by mRNA and miRNA to identify disease subtypes. CluF can be applied to stratify patients with any disease containing multiomic datasets. AVAILABILITY AND IMPLEMENTATION: Source code and datasets are available at https://github.com/GudaLab/iCluF_core.