The objective of the study was to determine optimal conditions for sampling, sample processing and mass-spectrometry based analysis of infants’ salivary peptidome. Saliva was sampled in 3- and 6-month-old infants and peptide extracts were prepared. Various sample pretreatments before profiling by MALDI-ToF were evaluated and peptide identification was undertaken by MALDI-ToF/ToF or nanoLC-ESI-IT tandem MS. A fast and simple protocol (cut-off filtration at 5 kDa) was satisfactory to produce extracts where no proteolysis was detected even when no protease inhibitor was added. Optimal MALDI spectra were generated after purification on C18 tips. Variability of spectra between two samples exceeded that of the technical replicates, validating that the method is suitable to conduct differential studies. Salivary peptides, identified by means of the two complementary mass spectrometry techniques, were fragments of proline-rich proteins and histatins. The fragments originated mainly from the C-terminal protein extremities. Indications on the proteolytic systems involved and the anatomic location where they intervene are proposed.