ABSTRACTMolecular methods offer superior sensitivity and specificity and reduce testing turnaround time from days to hours for detection ofBordetella pertussisandBordetella parapertussis. In this study, we evaluated the performance of the automated PCR-based AriesBordetellaAssay, which detects bothB. pertussisandB. parapertussisdirectly from nasopharyngeal swab specimens. The limits of detection (LoDs) were 1,800 CFU·ml−1forB. pertussisand 213 CFU·ml−1forB. parapertussis. The assay detected 16/18 uniqueB. pertussis/B. parapertussisstrains. Of 71 potentially cross-reacting organisms, 5 generated false positives in 1/6 replicates; none of 6 additionalBordetellaspp. were erroneously detected. Specimens were stable at 20 to 25°C for at least 10 h, at 4 to 8°C for 10 days, and at temperatures not exceeding −70°C for 6 months. Of 1,052 nasopharyngeal specimens from patients with suspected pertussis, 3.0% (n= 32) wereB. pertussispositive and 0.2% (n= 2) wereB. parapertussispositive. Combining these data with AriesBordetellaAssay data from 57 nasopharyngeal samples with previously confirmedB. pertussisorB. parapertussisdata and with data from 50 contrivedB. parapertussissamples, the proportions of positive and negative agreement of the respective Aries assays with the reference assays were 97.1% and 99.0% forB. pertussisand 100% and 99.7% forB. parapertussis. The AriesBordetellaAssay provides accurate detection and distinction ofB. pertussisandB. parapertussisinfections within 2 h. (This study has been registered at ClinicalTrials.gov under registration no. NCT02862262.)