Patients with lysosomal storage diseases (LSDs) suffer from physical and mental disabilities, which together with poor access to professional care may lead to impaired oral health. This cross-sectional case-control study characterized the status of oral health in patients with LSDs in Poland. Thirty-six children and young adults with various forms of LSDs were examined. The data were compared with those from age- and sex-matched healthy controls. Exemplary cases were presented to highlight typical problems in oral care associated with LSDs. When possible, saliva was collected and analyzed for total protein, inflammatory mediators, and antioxidant status. Generally, patients with LSDs had significantly higher prevalence of caries, inferior gingival status, and inadequate oral hygiene. The severity of oral health impairment in mucopolysaccaridoses, the most common LSD in Poland, was similar to that seen in patients with mannosidoses or Pompe disease. Saliva could be collected only from few less handicapped patients. In MPS, it did not appear to differ significantly from the controls, but in patients with Pompe disease it contained lower concentrations of vascular endothelial growth factor (VEGF) and monocyte chemoattractant protein-1 (MCP-1), but higher levels of tumor necrosis factor receptors 1 and 2 (TNF-R1, TNF-R2) and myeloperoxidase (MPO). In conclusion, Polish patients with LSDs have an inadequate level of oral hygiene and substantially deteriorated oral health.