The High Resolution Research Tomograph (HRRT) PET scanner is equipped with a moving Cs-137 transmission point source emitting 662 keV single photons. During post-injection transmission imaging 511 keV emission photons can be detected in the transmission window leading to gross underestimation of the reconstructed μ-value. Using cylindrical phantoms, methods to compensate for this emission contamination (EC) were investigated including histogram-based scaling and segmentation, while varying transmission window settings were used. Furthermore, the effects of subtracting a uniform or nonuniform EC estimation prior to transmission reconstruction were quantified. In conclusion, EC during HRRT transmission scans can lead to gross underestimation of μ-values, and the most accurate way to compensate for this is to combine nonuniform EC subtraction with transmission image segmentation. Emission contamination, image.