OBJECTIVE. The objective of our study was to quantify hepatic displacement between breath-holds in multiphasic contrast-enhanced MRI and assess the value of a 3D registration algorithm for displacement correction on subtracted images. MATERIALS AND METHODS. For this retrospective analysis, we evaluated MR images of 25 cirrhotic patients with treated hepatocellular carcinoma (HCC) and at least one coexisting small hepatic cyst that was hypointense on T1-weighted imaging. With the use of an automated 3D deformable registration algorithm, registered base and subtraction images were created using portal venous phase images as the baseline images. The relative displacement of the cysts over the dynamic phases was used to estimate hepatic displacement before and after registration. The width of the subtraction band artifact, HCC lesion conspicuity, and overall subtraction artifact level (i.e., image quality of the entire volume) of the subtraction images were evaluated before and after registration on a 5-point scale (1 = nondiagnostic, 5 = excellent image quality) by two blinded radiologists. Hepatic displacement and subtraction band artifact results were analyzed using the paired Student t test, and the results for HCC lesion conspicuity and image quality of the volume results were analyzed using the Wilcoxon signed rank test. Interobserver agreement was assessed using kappa statistics. RESULTS. The average total cyst displacement on unenhanced, arterial, and delayed phase images was significantly reduced by registration from 4.0, 3.2, and 4.6 mm, respectively, on pre-registered images to 2.4, 1.6, and 1.3 mm on postregistered images (p < 0.01). The mean HCC lesion conspicuity grade improved from 3.4 before registration to 4.4 after registration (p < 0.01), and the mean grade for image quality of the volume improved from 3.3 before registration to 4.6 after registration (p < 0.01). The average width of the subtraction band artifact decreased from 5.3 mm before registration to 2.4 mm after registration, from 6.1 mm before registration to 2.6 mm after registration, and from 5.2 mm before registration to 2.8 mm after registration for the arterial, portal venous, and delayed phase subtractions, respectively (p < 0.01). CONCLUSION. Automated registration of the liver in multiphasic MRI examinations reduced interphasic hepatic displacement, improved the conspicuity of the treated HCC lesion, and improved the overall subtraction image quality.