Tropheryma whipplei is the causative agent of classic Whipple's disease (WD) and other clinical entities, such as localized infection. Asymptomatic carriers have also been reported, mainly based on the testing of fecal samples. Our objective was to undertake a retrospective analysis of molecular biology usage for the diagnosis of WD over a 12-year period in our reference center. We tested 27,923 samples from 15,473 patients. The number of patients tested and the number of patients with a positive PCR result for T. whipplei have increased significantly over the last 12 years (P < 0.0001). Overall, T. whipplei was more frequently recovered from stools (43%), saliva (15%), duodenal biopsy samples (12.5%), blood (5%), and cerebrospinal fluid (CSF) (6%) and less commonly from cardiac valves (3%), urine (0.5%), skin biopsy samples (1%), lymph nodes (2.5%), aqueous humor (0.5%), and intra-articular fluid (1%). Among all the positive samples, we observed that stool samples and skin biopsy samples exhibited a higher prevalence of positivity by real-time quantitative PCR (qPCR) at 10.07% and 15.4%, respectively. The number of patients with a positive PCR result for T. whipplei has increased significantly over the last 12 years, although the positive ratio has not changed. Improvements in diagnostic tools have contributed greatly toward greater knowledge of WD and, consequently, the interest of physicians in this condition. In addition, we propose here an update of the diagnostic strategy for WD when qPCR is being used.