The aim was to examine the protein profiles of whole and parotid saliva using Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) and MALDI-TOF mass spectrometry. The banding patterns of proteins exhibited by the unstimulated whole saliva samples on the gel remained quite constant but the intensity of the protein bands were slightly different from one sample to another. Comparison of the protein profiles of unstimulated whole saliva and stimulated parotid saliva showed almost similar banding pattern. The exception is the presence of a pink protein band in the 65-67 kD region in the stimulated parotid saliva samples which was also observed in the unstimulated whole saliva sample contributed by a cerebral palsy patient. Analysis of the saliva samples using MALDI-TOF mass spectrometry also revealed that the stimulated parotid saliva samples exhibited some peaks that were in the same region as those for the unstimulated whole saliva sample of the cerebral palsy subject. This may imply that there is ineffective control of the parotid secretion in cerebral palsy subject under unstimulated condition. The SDS-PAGE and MALDI-TOF analyses may provide more information on the profiles of the salivary proteins which could be beneficial in the diagnosis of salivary gland dysfunction.