Bartonella spp. was first described as a possible cause of culture-negative endocarditis in 1993, and has since emerged as a significant cause of this condition worldwide. We describe a complicated case of culture-negative endocarditis in an immune-competent male patient, which was confirmed on resected heart valves to have been caused by Bartonella quintana by broad-range 16S ribosomal RNA polymerase chain reaction. The objective of this report is to highlight the clinical, diagnostic and therapeutic challenges of Bartonella endocarditis.