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To evaluate the dose values predicted by several calculation algorithms in two treatment planning systems, Monte Carlo (MC) simulations and measurements by means of various detectors were performed in heterogeneous layer phantoms with water- and bone-equivalent materials. Percentage depth doses (PDDs) were measured with thermoluminescent dosimeters (TLDs), metal-oxide semiconductor field-effect transistors (MOSFETs), plane parallel and cylindrical ionization chambers, and beam profiles with films. The MC code used for the simulations was the PENELOPE code. Three different field sizes (10 x 10, 5 x 5, and 2 x 2 cm2) were studied in two phantom configurations and a bone equivalent material. These two phantom configurations contained heterogeneities of 5 and 2 cm of bone, respectively. We analyzed the performance of four correction-based algorithms and one based on convolution superposition. The correction-based algorithms were the Batho, the Modified Batho, the Equivalent TAR implemented in the Cadplan (Varian) treatment planning system (TPS), and the Helax-TMS Pencil Beam from the Helax-TMS (Nucletron) TPS. The convolution-superposition algorithm was the Collapsed Cone implemented in the Helax-TMS. All the correction-based calculation algorithms underestimated the dose inside the bone-equivalent material for 18 MV compared to MC simulations. The maximum underestimation, in terms of root-mean-square (RMS), was about 15% for the Helax-TMS Pencil Beam (Helax-TMS PB) for a 2 x 2 cm2 field inside the bone-equivalent material. In contrast, the Collapsed Cone algorithm yielded values around 3%. A more complex behavior was found for 6 MV where the Collapsed Cone performed less well, overestimating the dose inside the heterogeneity in 3%-5%. The rebuildup in the interface bone-water and the penumbra shrinking in high-density media were not predicted by any of the calculation algorithms except the Collapsed Cone, and only the MC simulations matched the experimental values within the estimated uncertainties. The TLD and MOSFET detectors were suitable for dose measurement inside bone-equivalent materials, while parallel ionization chambers, applying the same calibration and correction factors as in water, systematically underestimated dose by 3%-5%.