(18) F-FDG and (68) Ga-citrate PET/CT have both been shown to be useful in the management of tuberculosis (TB). We compared the abnormal PET findings of (18) F-FDG- and (68) Ga-citrate-PET/CT in patients with TB. Methods Patients with TB on anti-TB therapy were included. Patients had a set of PET scans consisting of both (18) F-FDG and (68) Ga-citrate. Abnormal lesions were identified, and the two sets of scans were compared. The scan findings were correlated to the clinical data as provided by the attending physician. Results 46 PET/CT scans were performed in 18 patients, 11 (61 %) were female, and the mean age was 35.7 +/- 13.5 years. Five patients also had both studies for follow-up reasons during the use of anti-TB therapy. Thirteen patients were co-infected with HIV. (18) F-FDG detected more lesions than (68) Ga-citrate (261 vs. 166, p <0.0001). (68) Ga-citrate showed a better definition of intracerebral lesions due to the absence of tracer uptake in the brain. The mean SUVmax was higher for (18) F-FDG compared to (68) Ga-citrate (5.73 vs. 3.01, p <0.0001). We found a significant correlation between the SUVmax of lesions that were determined by both tracers (r = 0.4968, p <0.0001). Conclusion Preliminary data shows (18) F-FDG-PET detects more abnormal lesions in TB compared to (68) Ga-citrate. However, (68) Ga-citrate has better lesion definition in the brain and is therefore especially useful when intracranial TB is suspected.