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This technology addresses the limitations of two\u2010dimensional (2D) cultures, reduces species\u2010specific discrepancies, and is particularly valuable for investigating virus\u2013host interactions and pathogenic mechanisms under near\u2010physiological conditions. This review systematically outlines key advancements in organoid\u2010based virology, including the propagation of hard\u2010to\u2010culture pathogens such as human rhinovirus C (HRV\u2010C) and norovirus (NoV), as well as novel insights into viral pathogenesis, including the severe acute respiratory syndrome coronavirus 2 (SARS\u2010CoV\u20102) and Zika virus (ZIKV) infection, and the translational utility of organoids for antiviral drug screening and preclinical assessment. It further examines the use of organoids in modeling cancer and neurological diseases, compares the strengths and limitations of different cellular sources, and discusses their potential integration with emerging technologies such as CRISPR gene editing and 3D bioprinting. In addition, it maps a translational pathway from molecular mechanisms to clinical practice to facilitate the study of disease mechanisms and accelerate drug and vaccine development. Finally, holistic strategies are proposed to address existing challenges, such as the lack of immune components and inadequate vascularization. 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