In this paper, the pilot design aiming at mitigating the inter-cell interference in MIMO OFDM systems is addressed. We first compute the mean square error of the frequency domain LS joint channel estimation with the consideration of interfering cell. We then overview the optimal pilot sequences within a cell, which can cancel the intra-cell multiple access interference. Based on the mean square error and variation coefficient, we propose two conditions for the pilot design to mitigate the intercell interference. It is shown that if an ideal channel between interferer and receiver is assumed, we can obtain the pilots resulting in a smaller value of mean square error based on the variation coefficient of zero, which make the power of inter-cell interference distribute at all paths of the channel more uniformly and less, therefore, the performance on system level would be improved. A further discussion about proposed guidelines in practical system is made, and numerical calculations as well as simulation results are presented to verify the theoretical analysis.