To evaluate effect of respiration during acquisition of CT data on accurate localization of small focal hepatic lesions(FHLs) by comparing US performed during inspiration and expiration with fused CT images obtained during inspiration and expiration. Twenty-five patients(M:F=7:18, mean age=45 years) with 42 FHL(<3cm) such hemangiomas(n=29) and cysts(n=13) were collected. They underwent three-phase liver CT; arterial and portal phases were obtained during inspiration, while equilibrium phase was were obtained during expiration. Portal phase(inspiration CT=ICT) and equilibrium phase(expiration CT=ECT) images were uploaded separately in LOGIQ E9 equipped with Volume Navigation, After uploading ICT, plane and point registration were done during performing US during inspiration(inspiration US=IUS) and expiration(expiration US=EUS), respectively. The same process was repeated after uploading ECT. Accuracy of localization of each lesion was graded with three-point score according to size difference between CT and US(concordance ratio=CR). CR between CT/US in all combinations of respiration was compared. CRs of ICT/IUS vs. ICT/EUS were significantly different(p = .0005). Respiration state of US seemed not to affect CR when using ECT(p = .117). CRs were significantly lower in EUS than in IUS(p = .0007). Respiration state during obtaining CT might affect accurate localization of small FHLs. Accurate localization could be worse when US was performed during expiration.