Background: This work reports, for the first time, a validated methodology for qualitative and quantitative melatonin analyses directly from a complex matrix, namely rat milk, using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in a useful strategy for fast assessment of this molecular species. Methods: This novel approach uses the imaging feature of a MALDI instrument to create bidimensional images of a selected area. Results for sample concentration are expressed as a function of pixel-by-pixel intensity in grayscale, which are quantified according to pixel intensity through ImageJ open source software. For the extent of this work, two conditions were monitored: light-and dark-obtained milk.