This study evaluated the dosimetric impact of bone heterogeneity on the surface dose and dose prescription, when dose is assumed to be prescribed on a homogeneous medium in kV x-ray radiotherapy. A heterogeneous phantom containing a thin water layer (thickness = 1-5 mm) over a bone (thickness =1 cm) was used to mimic treatment sites of forehead, knee and chest wall. The phantom was irradiated by a 220 kVp photon beam with field size of 5 cm diameter. Percentage depth dose, surface dose and photon energy spectrum with different thicknesses of water were determined using Monte Carlo simulations (the EGSnrc code) with experimental verifications using parallel-plate ionization chamber and radiochormatic film. Our results (treatment cone of 5 cm diameter) showed that the surface dose increased in a range of 2.5-3.7% when the water layer above the bone was increased from 1 to 5 mm. However, the surface dose did not increase linearly with the increase of water thickness, and the maximum increase of surface dose was found at a water thickness of 3 mm. Results of the percentage depth dose showed that the maximum bone dose was about 210% higher than the surface dose in the heterogeneous phantom. It is concluded that in treatment sites having a thin layer of tissue over a bone in kV x-ray radiotherapy, if increased surface dose due to bone heterogeneity is not considered, this will result in an additional dosimetric uncertainty narrowing down the total error margin (5%).