Peptide-N4-(N-acetyl-α-glucosaminyl) asparagine amidases (commonly known as PNGases) have been described in a wide variety of prokaryotic hosts and exist as an integral part of the lysosomal refolding machinery in all higher organisms. Since the discovery of this ubiquitous biological function of PNGases 15 years ago, research on PNGases has found growing attention within and outside of the glycobiology research community, with currently more than 30 eukaryotic and bacterial PNGases identified and well studied. Based on the research results of their structures, enzyme properties and functions, PNGases can be primarily divided into three different types: PNGase F-like, acidic PNGases, and cytoplasmic PNGases. In this review, a brief summary of the current knowledge of these three types of PNGases in respect of their general properties and applications of the commercially available PNGases in glycopeptide and glycoprotein analysis will be presented.