Despite the development in NOx aftertreatment for Diesel engines, EGR is a cost-effective solution to fulfill current and future emission regulations. There is a wide bibliography discussing the global effects of EGR on combustion and emissions. However, little has been published concerning the effects of the unsuitable EGR and air distribution among cylinders. Since current HSDI engines operate with EGR rates as high as 50% the effect of the unequal EGR distribution becomes important. In addition, cylinder-to-cylinder charge dispersion becomes a critical aspect on the control of low temperature combustion systems. In concordance with the aspects outlined before, the aim of this paper is to study the effects of the EGR cylinder to cylinder distribution on the engine performance and emissions. To cope with this objective, experiments have been conducted in a HSDI engine with two different EGR systems. On the one hand, a High Pressure EGR system which produces high EGR cylinder-to-cylinder dispersion. On the other hand, a Low Pressure EGR system that allows a perfect EGR-air mixing before gas enters the cylinders. In the first part of the paper, the EGR distribution capabilities of each EGR system are determined. Then, comparing the engine emissions with both EGR architectures, the effects of differences in EGR rate and intake temperature of each cylinder are discussed.