In this study, large-scale profiling of salivary proteins and peptides ranging from 2 to 100 kDa was demonstrated using surface-enhanced laser desorption/ionization–time of flight–mass spectrometry (SELDI-TOF-MS). Results show that chip surface type and sample type critically affect the amount and composition of detected salivary proteins. Delayed processing time resulted in both increase and decrease of peak numbers consistent with proteolysis. SELDI-TOF-MS profiles also changed, depending on storage temperature, although sample processing by centrifugation and numbers of freeze–thaw cycles had a minimal impact. In conclusion, SELDI-TOF-MS offers a simple, rapid, high-throughput technique for profiling low-mass (<10 kDa) saliva proteins/peptides. We wish to use this technique to gain insight into the human saliva proteome composition and its changes over time in response to food consumption.