The purpose of this study is to validate Eclipse's electron Monte Carlo algorithm (eMC) in heterogeneous phantoms using radiochromic films and EGSnrc as a reference Monte Carlo algorithm. Four heterogeneous phantoms are used in this study. Radiochromic films are inserted in these phantoms, including in heterogeneous media, and the measured relative dose distributions are compared to eMC calculations. Phantoms A, B, and C contain 1D heterogeneities, built with layers of lung‐ (phantom A) and bone‐ (phantoms B and C) equivalent materials sandwiched in Plastic Water. Phantom D is a thorax‐anthropomorphic phantom with 2D lung heterogeneities. Electron beams of 6, 9, 12 and 18 MeV from a Varian Clinac 2100 are delivered to these phantoms with a 10×10 cm2 applicator. Monte Carlo simulations with an independent algorithm (EGSnrc) are also used as a reference tool for two purposes: (1) as a second validation of the eMC dose calculations, and (2) to calculate the stopping power ratio between radiochromic films and bone medium, when dose is measured inside the heterogeneity. Percent depth dose (PDD) film measurements and eMC calculations agree within 2% or 3 mm for phantom A, and within 3% or 3 mm for phantoms B and C for almost all beam energies. One exception is observed with phantom B and the 6 MeV, where measured PDDs and those calculated with eMC differ by up to 4 mm. Gamma analysis of the measured and calculated 2D dose distributions in phantom D agree with criteria of 3%, 3 mm for 9, 12, and 18 MeV beams, and criteria of 5%, 3 mm for the 6 MeV beam. Dose calculations in heterogeneous media with eMC agree within 3% or 3 mm with radiochromic film measurements. Six (6) MeV beams are not modeled as accurately as other beam energies. The eMC algorithm is suitable for clinical dose calculations involving lung and bone.PACS numbers: 87.10.Rt, 87.55.km