Diffusion has a clear effect on qT2 measurements especially at high resolutions, caused by the imaging gradients. SSE and MSME protocols were used to scan a phantom and an in-vivo brain. An equation representing the effective b value of the applied pulse sequence (MSME) was developed to estimate the attenuation of the signal caused by diffusion. T2 values calculated without correcting the diffusion effect showed high variability between scans with different parameter sets. After correction T2 values increased and showed excellent agreement. The method demonstrated here is generalized and can apply to different pulse sequences, it improves accuracy and stability.