Background Mucopolysaccharidoses (MPS) are rare, inherited lysosomal storage disorders characterized by progressive multiorgan involvement. Previous studies on incidence and prevalence of MPS mainly focused on countries other than the United States (US), showing considerable variation by country. This study aimed to identify MPS incidence and prevalence in the US at a national and state level to guide clinicians and policy makers. Methods This retrospective study examined all diagnosed cases of MPS from 1995 to 2015 in the US using the National MPS Society database records. Data included year of birth, patient geographic location, and MPS variant type. US population information was obtained from the National Center for Health Statistics. The incidence and prevalence rates were calculated for each disease. Incidence rates were calculated for each state. Results We obtained information from 789 MPS patients during a 20-year period. Incidence of MPS in the US was found to be 0.98 per 100,000 live births. Prevalence was found to be 2.67 per 1 million. MPS I, II, and III had the highest incidence rate at birth (0.26/100,000) and prevalence rates of 0.70–0.71 per million. Birth incidences of MPS IV, VI, and VII were 0.14, 0.04 and 0.027 per 100,000 live births. Conclusions This is the most comprehensive review of MPS incidence and prevalence rates in the US. Due to the large US population and state fragmentation, US incidence and prevalence were found to be lower than other countries. Nonetheless, state-level studies in the US supported these figures. Efforts should be focused in the establishment of a national rare disease registry with mandated reporting from every state as well as newborn screening of MPS.