The aim of the present work was to investigate absorbed and to calculate effective doses (EDs) in cone-beam computed tomography (CBCT). The study was conducted using examination protocols with and without lead apron shielding. A full-body male RANDO^® phantom was loaded with 110 GR200A thermoluminescence dosemeter chips at 55 different sites and set up in two different CBCT systems (CS 9500^®, ProMax^® 3D). Two different protocols were performed: the phantom was set up (1) with and (2) without a lead apron. No statistically significant differences in organ and absorbed doses from regions outside the primary beam could be found when comparing results from exposures with and without lead apron shielding. Consequently, calculating the ED showed no significant differences between the examination protocols with and without lead apron shielding. For the ProMax^® 3D with shielding, the ED was 149 µSv, and for the examination protocol without shielding 148 µSv (SD = 0.31 µSv). For the CS 9500^®, the ED was 88 and 86 µSv (SD = 0.95 µSv), respectively, with and without lead apron shielding. The results revealed no statistically significant differences in the absorbed doses between examination with and without lead apron shielding, especially in organs outside the primary beam.