Background: Previous reports have highlighted the high prevalence of blood culture negative endocarditis (BCNE) in South Africa.Methods: The Tygerberg Endocarditis cohort (TEC) study is a prospective cohort study of patients with confirmed or suspected IE presenting to Tygerberg Academic Hospital, Cape Town, South Africa. Results: To date, 44 patients have been included in this ongoing study. Fourteen of the 44 patients (31.8%) had BCNE. Further analysis of the patients with BCNE identified Bartonella species as the most common causative organism (n=6; 43%). Other causes included Mycoplasma species (n=2), C. burnetii (n=1), and non-bacterial thrombotic endocarditis due to anti-phospholipid syndrome (n=1). No cause could be identified in 4 of the 44 patients (9%). Bartonella quintana was identified with PCR of valvular tissue as the causative organism in 4 of the 5 patients that underwent urgent surgery. The patients with Bartonella IE (n=6) had an average age of 39 years with equal gender distribution The common clinical features were clubbing (n=5; 83%), anemia (n=4; 66.6%), haematuria (n=3; 50%), acute on chronic severe valvular lesion (n=3; 50%) and acute severe valvular lesion (n=2; 33.3%). The aortic valve was involved in 5 of 6 patients. During a mean follow-up period of 251 days after diagnosis, no major adverse events occurred.Conclusion: Bartonella IE is an important cause of BCNE in the Western Cape of South Africa. Imaging findings of significant valvular destruction with large vegetations on the aortic valve not affected by pre-existing congenital or rheumatic valve disease, should raise the suspicion of Bartonella IE.