This paper presents an in-vivo accuracy study on combining skin markers (external fiducials) and fiducial needles (internal fiducials) for motion compensation during liver interventions. We compared the target registration error (TRE) for different numbers of skin markers n(s) and fiducial needles n(f), as well as for different transformation types, in two swine using the tip of an additional tracked needle as the target. During continuous breathing, n(f) had the greatest effect on the accuracy, yielding mean root mean square (RMS) errors of 4.8 +/- 1.1 mm (n(f) = 0), 2.0 +/- 0.9 mm (n(f) = 1) and 1.7 +/- 0.8 mm (n(f) = 2) when averaged over multiple tool arrangements (n = 18, 36, 18) with n(s) = 4. These values correspond to error reductions of 11%, 64% and 70%, respectively, compared to the case when no motion compensation is performed, i.e., when the target position is assumed to be constant. At expiration, the mean RMS error ranged from 1.1 mm (n(f) = 0) to 0.8 mm (n(f) = 2), which is of the order of magnitude of the target displacement. Our study further indicates that the fiducial registration error (FRE) of a rigid transformation reflecting tissue motion generally correlates strongly with the TRE. Our findings could be used in practice to (1) decide on a suitable combination of fiducials for a given intervention, considering the trade-off between high accuracy and low invasiveness, and (2) provide an intra-interventional measure of confidence for the accuracy of the system based on the FRE.