We will present a synthesis of the results of our study aiming at evaluating the impact of the cultivation of different maize genotypes (Monumental, DKC3420, DK315, DKC5143, DKC5783) and of corresponding Bt-maize genotypes tolerant to the pyrale production (Mon810, TXP138-F, DKc3946, DK5018, DKc5783Bt), on soil microflora. This analysis has been conducted on three compartments: the soil, the rhizosphere (defined as the soil in contact with the root) and the root (colonisation by arbuscular mycorrhizal fungi).This study has been performed in a greenhouse experiment settled to estimate the impact produced by the cultivation of the different maize genotypes on: (i) global microbial indicators, such as the structure of soil bacterial and fungal communities and (ii) functional microbial communities responsible for denitrification (narG), degradation of pesticides (herbicide atrazine, atzC) and arbuscular mycorhizal symbiosis.This integrated approach allowed the estimation of the impact of the cultivation of Bt-maize genotypes relative to that produced by the cultivation of different genotypes of maize on the structure and the functioning of soil microbial communities, notably those promoting plant growth and health which are key elements of soil fertility.