This study evaluated a novel non-verbal communication method for people with severe motor and intellectual disabilities (SMID) based on a biochemical marker, salivary amylase. The physical and psychological status of 10 people with SMID was quantitatively evaluated using a hand-held salivary amylase activity monitor. Each patient needed daily gastric and/or bronchial tube exchanges and these medical procedures were thought to cause severe distress and pain. Salivary amylase activity and heart rate were simultaneously measured during 32 medical procedures. The medical procedures resulted in a significant mean increase for individuals of 70% in salivary amylase activity. The increase in salivary amylase activity was more than four-fold that observed for heart rate. The structural equation modelling analysis also demonstrated a significant correlation between pain and salivary amylase activity. Our data indicate that salivary amylase activity might be used as a non-verbal method of assessing pain in people with SMID.