Registration and fusion guided by the fiducial markers of SPECT and CT images acquired via distinct equipment is a common practice in several nuclear medicine centres. In this study, five different fiducial configurations were studied and compared for SPECT and CT image acquisitions: iodide-131 (131I) within a needle cap, 131I associated with cotton, a lead and a ceramic aluminium sphere or mixed with an agarose solution. Fiducials that employed agarose mixtures presented the lowest dpr values (between 0.34 and 0.53 mm) and better homogeneous regions in both images to perform registration. In addition, this assembly exhibited the lowest global mean dpr and standard deviations in Gaussian adjustments. In comparison with the other configurations, the agarose dpr was statistically lower than that of cotton, ceramic aluminium and just 131I for all the six landmarks. Despite its similarity with the lead sphere configuration, for five of the landmarks, agarose showed no artefacts in CT and more homogeneous regions of interest in SPECT images. In addition, agarose demonstrated great reproducibility to guide point-based registration processes.