Background: Lysosomal storage disorders (LSD) are storage disorders involving malfunction of degradation enzymes in lysosome. More than 50 types of LSD have been discovered, which includes the group of mucopolysaccharidoses (MPS), sphingolipidoses, oligosaccharidoses, mucolipidoses, lipoprotein storage disorders, lysosomal transport defects and neuronal ceroid lipofuscinoses and others. The aims of this study were to calculate the birth prevalence and carrier frequency of LSDs in the Malaysian population; to compare our results with reported epidemiologic data from other populations, and to describe the mutation spectrum in Malaysia. From 2008 to 2017, 2.1% (92/4338) suspected patients were diagnosed with LSD. Results: The prevalence of LSD in Malaysia was 1/231,904 live births. The combined prevalence of MPS was 1/292,401 with its subtype of MPS II presented the highest calculated birth prevalence of 1/221,425. Within the group of sphingolipidoses, the combine prevalence was 1/770,777 with Fabry as the most common disorder with calculated prevalence of 1/193,203 followed by metachromatic leukodystrophy (MLD) (1/494,514). MLD is more common among people of Iban ethnicity with the prevalence of 1/6,981. Pompe and mucolipidoses type II are the less common subtypes of LSD with a prevalence of 1/1,694,634 and 1/2,229,516, respectively.Conclusion: Overall, although the prevalence of LSD in Malaysia may be underestimated, the prevalence of MPS is consistent with other reported in East Asian countries.