Introduction diabetes mellitus is associated with a high prevalence of oral infections. However, it is unclear how diabetes impacts oral innate antimicrobial proteins. This study evaluated salivary lysozyme and histatins, two major innate antimicrobial proteins, in patients with diabetes and non-diabetic controls. Methods a cross-sectional study where salivary lysozyme and histatins were measured alongside plasma glucose levels. Values of the salivary proteins were compared between the two groups; their association with glucose levels was also established using correlation and regression analysis. Results one hundred and fifty-one participants were recruited for this study, 85 (56.3%) of them had type 2 diabetes mellitus with a median fasting plasma glucose of 108.8 mg/dl (IQR 91.2-134.8) while the remaining 66 (43.7%) healthy non-diabetic controls had a median random plasma glucose of 101 mg/dl (IQR 89-112). The median salivary lysozyme was 32.5 ng/ml (IQR 25.0-39.6) in the group with diabetes and 36.4 ng/ml (IQR 31.4-42.1; p=0.01) in the non-diabetic control group. The median salivary histatins was 9.2 ng/ml (IQR 7.6 -10.2) in the group with diabetes and 14.7 ng/ml (IQR12.8-16.5; p<0.001) in the non-diabetic control group. Salivary lysozyme (r = -0.127; p =0.163) and histatins (r = -0.025; p = 0.424) were both negatively correlated with plasma glucose levels, and logistic regression showed that patients with diabetes are more likely to have lower levels of salivary lysozyme (0.957; p=0.013) and histatins (0.527; p<0.001). Conclusion patients with diabetes had reduced levels of salivary lysozyme and histatins, this could provide an insight into the associated high oral infection rates.