We characterized the distribution of minor elements such as Si and Fe in Al utilizing a nanoindentation and electron microscopy with an energy dispersed X-ray spectroscopy (EDS) system. Nanoindentation can detect the dislocation nucleation known as “pop-in” event, the critical load (Pc) depends on the solute amount of Fe. However, that in Si-doped Al is rarely changed up to 1.0 at% of Si. That independent Pc in Al-Si is caused by the inhomogeneity of the Si, which is the grain boundary segregation, in Al. The grain boundary segregation of Si was clearly detected by using a newly developed microcalorimeter type EDS system, even at the 0.1 at% Si.