Background: To improve therapy outcome of Yttrium-90 selective internal radiation therapy (90 Y SIRT), patientspecific post-therapeutic dosimetry is required. For this purpose, various dosimetric approaches based on different available imaging data have been reported. The aim of this work was to compare post-therapeutic 3D absorbed dose images using Technetium-99m (99m Tc) MAA SPECT/CT, Yttrium-90 (90 Y) bremsstrahlung (BRS) SPECT/CT, and 90 Y PET/CT. Methods: Ten SIRTs of nine patients with unresectable hepatocellular carcinoma (HCC) were investigated. The 99m Tc SPECT/CT data, obtained from 99m Tc-MAA-based treatment simulation prior to 90 Y SIRT, were scaled with the administered 90 Y therapy activity. 3D absorbed dose images were generated by dose kernel convolution with scaled 99m Tc/ 90 Y SPECT/CT, 90 Y BRS SPECT/CT, and 90 Y PET/CT data of each patient. Absorbed dose estimates in tumor and healthy liver tissue obtained using the two SPECT/CT methods were compared against 90 Y PET/CT. Results: The percentage deviation of tumor absorbed dose estimates from 90 Y PET/CT values was on average − 2 ± 18% for scaled 99m Tc/ 90 Y SPECT/CT, whereas estimates from 90 Y BRS SPECT/CT differed on average by − 50 ± 13%. For healthy liver absorbed dose estimates, all three imaging methods revealed comparable values. Conclusion: The quantification capabilities of the imaging data influence 90 Y SIRT tumor dosimetry, while healthy liver absorbed dose values were comparable for all investigated imaging data. When no 90 Y PET/CT image data are available, the proposed scaled 99m Tc/ 90 Y SPECT/CT dosimetry method was found to be more appropriate for HCC tumor dosimetry than 90 Y BRS SPECT/CT based dosimetry.