Treatment verification is a prerequisite for the verification of complex treatments, checking both the treatment planning process and the actual beam delivery. Pretreatment verification can detect errors introduced by the treatment planning system (TPS) or differences between planned and delivered dose distributions. In a previous paper we described the reconstruction of three-dimensional (3-D) dose distributions in homogeneous phantoms using an in-house developed model based on the beams delivered by the linear accelerator measured with an amorphous silicon electronic portal imaging device (EPID), and a dose calculation engine using the Monte Carlo code XVMC. The aim of the present study is to extend the method to situations in which tissue inhomogeneities are present and to make a comparison with the dose distributions calculated by the TPS. Dose distributions in inhomogeneous phantoms, calculated using the fast-Fourier transform convolution (FFTC) and multigrid superposition (MGS) algorithms present in the TPS, were verified using the EPID-based dose reconstruction method and compared to film and ionization chamber measurements. Differences between dose distributions were evaluated using the gamma-evaluation method (3%/3 mm) and expressed as a mean gamma and the percentage of points with gamma> 1 (P(gamma>1)). For rectangular inhomogeneous phantoms containing a low-density region, the differences between film and reconstructed dose distributions were smaller than 3%. In low-density regions there was an overestimation of the planned dose using the FFTC and MGS algorithms of the TPS up to 20% and 8%, respectively, for a 10 MV photon beam and a 3 x 3 cm2 field. For lower energies and larger fields (6 MV, 5 x 5 cm2), these differences reduced to 6% and 3%, respectively. Dose reconstruction performed in an anthropomorphic thoracic phantom for a 3-D conformal and an IMRT plan, showed good agreement between film data and reconstructed dose values (P(gamma>1) <6%). The algorithms of the TPS underestimated the dose in the low-dose regions outside the treatment field, due to an implementation error of the jaws and multileaf collimator of the linac in the TPS. The FFTC algorithm of the TPS showed differences up to 6% or 6 mm at the interface between lung and breast. Two intensity-modulated radiation therapy head and neck plans, reconstructed in a commercial phantom having a bone-equivalent insert and an air cavity, showed good agreement between film measurement, reconstructed and planned dose distributions using the FFTC and MGS algorithm, except in the bone-equivalent regions where both TPS algorithms underestimated the dose with 4%. Absolute dose verification was performed at the isocenter where both planned and reconstructed dose were within 2% of the measured dose. Reproducibility for the EPID measurements was assessed and found to be of negligible influence on the reconstructed dose distribution. Our 3-D dose verification approach is based on the actual dose measured with an EPID in combination with a Monte Carlo dose engine, and therefore independent of a TPS. Because dose values are reconstructed in 3-D, isodose surfaces and dose-volume histograms can be used to detect dose differences in target volume and normal tissues. Using our method, the combined planning and treatment delivery process is verified, offering an easy to use tool for the verification of complex treatments.