Clinical diagnostic testing for congenital central hypoventilation syndrome (CCHS) usually involves amplification and detection by (1) targeted mutation analysis or (2) sequence analysis. Test method performance differences are more pronounced when studying difficult templates [eg, guanine-cytosine (GC)-rich regions] or samples with abnormal allele ratios (eg, mosaicism). CCHS, an autosomal dominant disorder with identified mosaic carriers, is caused by expansion mutations of the GC-rich polyalanine-coding region of the PHOX2B gene in greater than 90% of patients (and other PHOX2B mutations in remaining patients). The combination of a GC-rich testing region and known mosaicism in CCHS necessitates the determination of the limit of detection for diagnostic tests. This study compared the limit of detection in CCHS-PHOX2B testing for both targeted mutation analysis and sequence analysis. Test samples included 6 differentially sized PHOX2B expansion mutations and 1 PHOX2B deletion mutation, all diluted over a range of concentrations; and 2 mosaic dyads. The limit of detection for PHOX2B expansion mutations was 1% and 20% mutant allele concentration with targeted mutation analysis and sequence analysis, respectively. These results indicate that PHOX2B testing using targeted mutation analysis is more likely to identify even low-level mosaicism for polyalanine expansion and deletion mutations. However, sequencing of PHOX2B is required to detect single base-pair mutations that cause the remaining small subset of CCHS cases. A combination of both the tests may be required in cases in which 1 test fails to identify the disease-causing mutation. These results can help guide clinicians when choosing a CCHS/PHOX2B clinical diagnostic testing method and interpreting results.