Five species of Bartonella have been reported to infect humans and cause a variety of diseases that can be difficult to diagnose. Four species of Bartonella have been reported to infect cats and dogs, and two of these species are considered to be zoonotic pathogens. Diagnosis of Bartonella infections is hampered by the slow, fastidious growth characteristics of Bartonella species. We report on the development of a single-step PCR-based assay for the detection and differentiation of medically relevant Bartonella species. PCR-mediated amplification of the 16S-23S rRNA intergenic region resulted in a product of a unique size for each Bartonella species, thereby allowing differentiation without the necessity of restriction fragment length polymorphism analysis or sequencing of the amplified product. The ability of the single-step PCR assay to differentiate between Bartonella species was determined with characterized isolates and blood samples from animals known to be infected with either Bartonella henselae, B. clarridgeiae, or B. vinsonii subsp. berkhoffii. The sensitivity of the single-step PCR assay relative to that of in vitro culture was determined with blood samples from B. henselae-infected cats. B. henselae target DNA was amplified from 100% of samples with greater than 50 CFU/ml and 80% of samples with 10 to 30 CFU/ml. The single-step assay described in the report expedites PCR-based detection and differentiation of medically relevant Bartonella species.