Two mutations in the MCOLN1 mucolipidosis IV (ML IV) gene represent ϳ95% of the mutations in Ashkenazi-Jewish patients with ML IV. The mutations , a splice site mutation (IVS3-2A>G) and an ϳ6.4-kb deletion (511del6434) , account for 72% and 23% of ML IV alleles in this population , respectively. An automated high-throughput assay was developed using the 5-nuclease (TaqMan) method for the simultaneous detection of both mutations in a single reaction. Three fluorescent probes specifically detected wild-type , IVS3-2A>G , and 511del6434 alleles in each reaction real-time. Data collected were automatically analyzed , and genotype results were uploaded into a laboratory information management system. The assay was validated using genomic controls , demonstrating high robustness and accuracy. Carrier screening of 10 ,527 samples revealed 77 heterozygote carriers of IVS3-2A>G , 25 heterozygote carriers of 511del6434 , and two compound heterozygote of both mutant alleles. The frequency of mutated alleles was 0.73% for IVS3-2A>G and 0.24% for 511del6434. The combined carrier frequency was 1:103 with predicted disease incidence of 1:42 ,436 individuals in this population , slightly lower than previously described frequencies. This automated high-throughput assay is labor saving , because two mutations can be detected in a single reaction. The method has potential for use in other assays requiring simultaneous detection of two mutations.