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Ultraviolet (UV) light-emitting diodes (UV-LEDs), a disinfection technology, efficiently inactivate pathogens in water. However, the assessment of UV-LED treatment and the mechanisms of UV inactivation on viruses (especially enveloped viruses) are limited. In this study, the efficiency of UV-LED treatment (at 280 and 265 nm) on various viruses with different capsid and genome structures, including Aichivirus [AiV], coxsackievirus B3 [CV.B3], PhiX174 bacteriophage [PhiX174], T4 bacteriophage [T4], mouse hepatitis virus (MHV), and Pseudomonas Phi6 bacteriophage [Phi6], was investigated. Based on the fluence, all forms of tested viruses (non-enveloped and enveloped) were more sensitive to UV-LEDs at 265 nm than at 280 nm. Among the tested non-enveloped viruses, T4 was more sensitive to UV treatment (both at 280 nm and 265 nm) than the other viruses (AiV, CV.B3, and PhiX174). Between the enveloped viruses (MHV and Phi6), Phi6 was much more UV-LED-resistant (both at 280 nm and 265 nm) than MHV. Capsid integrity (RT-)qPCR was used to investigate the effects of UV-LED treatment on the virus structure, suggesting that capsid damage is less important in virus inactivation by UV-LEDs for both virus groups. Moreover, the lipid bilayer of enveloped viruses may not influence the efficiency of UV-LED treatment. Viral genomic properties (e.g., length, nucleic acid content, and structure) are considered key factors for virus sensitivity to UV-LED treatment.