Volatile sulfur compounds (VSCs), which are major sources of oral malodor, are produced by putrefactive activities of bacteria. Saliva provides easily degradable protein substrates, and most proteins are glycosylated. We hypothesized that oral malodor would be associated with enhanced proteolysis or deglycosylation in saliva. The purpose of this study was to evaluate properties of glycoproteins in saliva and assess their association with VSC levels. Subjects were 88 patients who visited "the Fresh Breath Clinic", Dental Hospital, Tokyo Medical and Dental University. They were classified into malodor (n = 67) and non-malodor (n = 21) groups. After collecting saliva, the amounts of the total proteins and carbohydrate were determined. Molecular size distributions of salivary proteins/glycoproteins were analyzed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). The amount of the total salivary proteins was significantly higher in the malodor group. Major proteins/glycoproteins observed in SDS-PAGE analyses showed similar distributions between the two groups. In the malodor group, the salivary protein concentrations were positively correlated with the CH3SH levels (p < 0.05), and the carbohydrate contents were negatively correlated with the H2S levels (p < 0.05). These results indicated the possibility that salivary proteins/glycoproteins might be related to the malodor generation.