Mass spectrometry imaging (MSI) enables label-free, spatially -resolved analysis of molecules in biological samples. MSI coupled with soft ionization techniques provides two-and threedimensional maps of intact molecular ions, which greatly simplifies mass spectra and facilitates identification of molecules extracted from the sample. However, differences in ionization efficiencies of biomolecules and signal suppression during ionization, also referred to as "matrix effects," represent a challenge for quantitative MSI (Q-MSI) experiments. In this review, we summarize the current understanding of matrix effects in MSI and discuss different quantification strategies. We emphasize that using internal standards in Q-MSI is essential for accurate imaging and quantification of molecules in chemically complex samples. The ability to localize, identify, and quantify molecules in tissue sections and cells opens up unique opportunities for molecular-level understanding of biological processes, elucidation of disease mechanisms, understanding drug interactions with living organisms, and controlling synthesis of natural products. These capabilities make Q-MSI a powerful tool for biological research, clinical studies, and drug development.