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Simple Summary: The prognosis of intrahepatic cholangiocarcinoma (ICC) depends on tumor biology, morphology, and the high rates of late diagnosis and recurrence after curative-intent surgery, with high heterogeneity. Understanding the molecular landscape of ICC and its clinical implications for treatment and prognosis remains a major challenge. Several attempts have been made to classify molecular ICC subtypes, but they have produced heterogeneous results and need a clear clinical definition. This systematic review examined the evidence for the multi-omics-based classification of ICC to assess its clinical and prognostic significance. Molecular analysis of ICC can assist in decision-making by identifying patients who are suitable for targeted pre- and postoperative chemotherapy. Identifying clinical characteristics associated with specific ICC clusters resulting from multi-omics analysis could help tailor patient management. However, there are logistical, technical, and therapeutic challenges in the routine application of ICC molecular characterization. Identifying clinical characteristics commonly found in specific ICC clusters can help define high-risk ICC subtypes quickly and assist in selecting patients who may benefit the most from molecular profiling in the disease's earlier stages. Intrahepatic cholangiocarcinoma (ICC) is a heterogeneous disease characterized by a dismal prognosis. Various attempts have been made to classify ICC subtypes with varying prognoses, but a consensus has yet to be reached. This systematic review aims to gather relevant data on the multi-omics-based ICC classification. The PubMed, Embase, and Cochrane databases were searched for terms related to ICC and multi-omics analysis. Studies that identified multi-omics-derived ICC subtypes and investigated clinicopathological predictors of long-term outcomes were included. Nine studies, which included 910 patients, were considered eligible. Mean 3- and 5-year overall survival were 25.7% and 19.6%, respectively, for the multi-omics subtypes related to poor prognosis, while they were 70.2% and 63.3%, respectively, for the subtypes linked to a better prognosis. Several negative prognostic factors were identified, such as genes' expression profile promoting inflammation, mutations in the KRAS gene, advanced tumor stage, and elevated levels of oncological markers. The subtype with worse clinicopathological characteristics was associated with worse survival (Ref.: good prognosis subtype; pooled hazard ratio 2.06, 95%CI 1.67–2.53). Several attempts have been made to classify molecular ICC subtypes, but they have yielded heterogeneous results and need a clear clinical definition. More efforts are required to build a comprehensive classification system that includes both molecular and clinical characteristics before implementation in clinical practice to facilitate decision-making and select patients who may benefit the most from comprehensive molecular profiling in the disease's earlier stages. [ABSTRACT FROM AUTHOR]