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OBJECTIVE: Patients with mucopolysaccharidosis present several alterations of the stomatognathic complex, however, no data is available on saliva biochemistry and yeast colonization. The aim of the study was to evaluate caries experience as well as saliva biochemistry and microbiology parameters in patients with mucopolysaccharidosis. METHOD: The sample consisted of twelve participants with mucopolysaccharidosis followed in the Metabolic Disease Unit of the Centro Hospitalar de S. João and twelve healthy participants followed at the Faculty of Dental Medicine, University of Porto. To all participants, Decayed, Missing, Filled Teeth (DMFT) index was evaluated. In addition, saliva was collected to evaluate biochemical parameters (flow rate, pH, sodium, potassium, chloride, calcium, phosphate, α-amylase and IgA) and the microbiological profile (total microorganisms, mutans streptococci and yeasts) of all participants. RESULTS: In comparison to controls, the mucoplysacharidosis patients presented a higher prevalence of decayed teeth, lower salivary flow and pH values. They also presented also lower calcium and higher phosphate ions in saliva. No differences were found between groups regarding oral microbial load for total microorganisms, mutans streptococci and yeasts as well as oral prevalence of mutans streptococci. However, MPS patients presented higher prevalence of oral Candida in comparison to controls. CONCLUSION: The higher prevalence of decayed teeth and higher oral yeast colonization in MPS patients may be related to the lower saliva calcium concentration, pH and flow.