There are several reasons for hyposalivation, each affecting the salivary composition in different ways. The aim of this study was to analyze and compare lactoferrin, amylase and mucin MUC5B in stimulated whole saliva collected from subjects with hyposalivation of different origins and to relate the results to the presence of some microbial species associated with oral disorders. Albumin was determined as a marker of serum leakage. The characteristic feature for subjects with radiation-induced hyposalivation was a large increase in lactoferrin, probably due to leakage through inflamed mucosal tissues, while it was a high albumin content for the group with primary Sjögren's syndrome, probably due to disruption of the fragile mucosa. The saliva composition in subjects with hyposalivation of unknown origin or due to medicines was close to that in the healthy controls. All three hyposalivation groups tended to display a decrease in the concentrations of MUC5B and amylase. None of the microbial species analyzed (streptococci, mutans streptococci, Lactobacillus spp., Fusobacterium nucleatum, Prevotella intermedia/Prevotella nigrescens, Candida albicans, Staphylococcus aureus and enterics) correlated with concentration of MUC5B in saliva. The RT group, having the highest concentration of lactoferrin, had the lowest median number of F. nucleatum and was the only group in which median number of P. intermedia/P. nigrescens was zero.