The local structure in high temperature superconductors is nowadays considered a key point for understanding superconductivity mechanism. MgB2 has a well-known simple structure; but its local structure remains quite unexplored. This is due to the fact that typical x-ray local probes, such as EXAFS, fail when used to study local structure of light atoms, such as Mg and B. We used high resolution neutron diffraction with pair distribution function (PDF) analysis for investigating disorder on the atomic scale in the Al doped Mg1-xAlxB2 system. The results indicate an anisotropic structural inhomogeneity along the c-axis that could be related with the delocalized metallic-type bonding between Boron layers.