In this work, we present a study of the typical spontaneous defects present in self-assembled colloidal monolayers grown from polystyrene and silica microspheres. The quality of two-dimensional crystals from different colloidal suspensions of beads around 1 μm in diameter has been studied qualitatively and quantitatively, evaluated in 2D hexagonal arrays at different scales through Fourier analysis of SEM images and optical characterization. The crystallographic defects are identified to better understand their origin and their effects on the crystal quality, as well as to find the best conditions colloidal suspensions must fulfill to achieve optimal quality samples.