<p>High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration present a substantial challenge, as traditional methods like sample exclusion or imputation often compromise biological diversity and dependencies. Furthermore, the critical task of accurately classifying new patients with partial omics data into existing subtypes is commonly overlooked. To address these issues, we introduce Integrate Any Omics (IntegrAO), an unsupervised framework for integrating incomplete multi-omics data and classifying new samples. IntegrAO first combines partially overlapping patient graphs from diverse omics sources and utilizes graph neural networks to produce unified patient embeddings. Our systematic evaluation across five cancer cohorts involving six omics modalities demonstrates IntegrAO’s robustness to missing data and its accuracy in classifying new samples with partial profiles. An acute myeloid leukaemia case study further validates its capability to uncover biological and clinical heterogeneities in incomplete datasets. IntegrAO’s ability to handle heterogeneous and incomplete data makes it an essential tool for precision oncology, offering a holistic approach to patient characterization.</p>