Saliva is a complex multifunctional fluid that bathes the oral cavity to assist in soft and hard tissue maintenance, lubrication, buffering, defence against microbes and initiating digestion of foods. It has been extensively characterised in humans but its protein composition in dogs remains poorly characterised, yet could explain (patho) physiological differences between individuals, breeds and with humans. This pilot discovery study aimed to characterise canine saliva from two breeds, Labrador retrievers and Beagles, and to compare this with human saliva using quantitative mass spectrometry. The analysis demonstrated considerable inter-individual variation and difference between breeds, however these were small in comparison to the differences between species. Functional mapping suggested roles of detected proteins similar to those found in human saliva with the exception of the initiation of digestion as salivary amylase was lacking or at very low abundance in canine saliva samples. Many potential anti-microbial proteins were detected agreeing with the notion that the oral cavity is under continuous microbial challenge. This article is protected by copyright. All rights reserved.