© Cambridge University Press 2016 Purpose: To develop a software program to convert physical dose distribution into biological effective dose (BED). Methods: The MATLAB-based BED distribution software program was designed to import the radiotherapy treatment plan from the computer treatment planning system and to convert the physical dose distribution into the BED distribution. The BED calculation was based on the linear-quadratic-linear model (LQ-L model). Besides radiobiological parameters, other specific data could be fed in through the panel. The accuracy of the program was verified by comparing the BED distribution with manual calculation. Results: This software program was able to import the radiotherapy treatment plans and pull out pixel-wised physical dose for BED calculation, and display the isoBED lines on the computed tomographic (CT) image. The verification of BED dose distribution was performed in both phantom and clinical cases. It revealed that there were no differences between the program and manual BED calculations. Conclusion: It is feasible and practical to use this in-house BED distribution software program in clinical practices and research work. However, it should be used with caution as the validity of the program depends on the accuracy of the published biological parameters.