Acid hydrolase activities are normally confined within the cell to the lysosome, a membrane-delimited cytoplasmic organelle primarily responsible for the degradation of macromolecules. However, lysosomal proteins are also present in human plasma and a proportion of these retain mannose 6-phosphate (Man6-P), a modification on N-linked glycans that is recognized by Man6-P receptors (MPRs) that normally direct the targeting of these proteins to the lysosome. In this study, we have purified the Man6-P glycoforms of proteins from human plasma by affinity chromatography on immobilized MPRs and characterized this subproteome by two-dimensional gel electrophoresis and by tandem mass spectrometry. As expected, we identify many known and potential candidate lysosomal proteins. In addition, we also identify a number of abundant classical plasma proteins that were retained even after two consecutive rounds of affinity purification. Given their abundance in plasma, we initially considered these proteins to be likely contaminants but a mass spectrometric study of Man6-phosphorylation sites using MPR-purified glycopeptides revealed that some proportion of these classical plasma proteins contain the Man6-P modification. We propose that these glycoproteins are phosphorylated at low levels by the lysosomal enzyme phosphotransferase but their high abundance results in detection of Man6-P glycoforms in plasma. These results may provide useful insights into the molecular processes underlying Man6-phosphorylation and highlight circumstances under which the presence of Man6-P may not be indicative of lysosomal function. In addition, characterization of the plasma Man6-P glycoproteome should facilitate development of mass spectrometry-based tools for the diagnosis of lysosomal storage diseases and for investigating the involvement of Man6-P containing glycoproteins in more widespread human diseases and their potential utility as biomarkers.