Potential etiological relevance for gastroenteric disorders including diarrhea has been assigned toArcobacter butzleri. However, standard routine diagnostic algorithms for stool samples of patients with diarrhea are rarely adapted to the detection of this pathogen and so,A. butzleriis likely to go undetected unless it is specifically addressed, e.g., by applying pathogen-specific molecular diagnostic approaches. In the study presented here, we compared three real-time PCR assays targeting the geneshsp60,rpoB/C(both hybridization probe assays) andgyrA(fluorescence resonance energy transfer assay) ofA. butzleriin a test comparison without a reference standard using a stool sample collection with a high pretest probability from the Ghanaian endemicity setting. Latent class analysis was applied with the PCR results obtained with a collection of 1495 stool samples showing no signs of PCR inhibition to assess the real-time PCR assays’ diagnostic accuracy. Calculated sensitivity and specificity were 93.0% and 96.9% for thehsp60-PCR, 100% and 98.2% for therpoB/C-PCR, as well as 12.7% and 99.8% for thegyrA-PCR, respectively. The calculatedA. butzleriprevalence within the assessed Ghanaian population was 14.7%. As indicated by test results obtained with high-titer spiked samples, cross-reactions of thehsp60-assay andrpoB/C-assay with phylogenetically related species such asA. cryaerophiluscan occur but are less likely with phylogenetically more distant species like, e.g.,A. lanthieri. In conclusion, therpoB/C-assay showed the most promising performance characteristics as the only assay with sensitivity >95%, albeit associated with a broad 95%-confidence interval. In addition, this assay showed still-acceptable specificity of >98% in spite of the known cross-reactivity with phylogenetically closely related species such asA. cryaerophilus. If higher certainty is desired, thegyrA-assay with specificity close to 100% can be applied for confirmation testing with samples showing positiverpoB/C-PCR results. However, in case of a negative result in thegyrA-assay, this cannot reliably exclude the detection ofA. butzleriin therpoB/C-assay due to thegyrA-assay’s very low sensitivity.