Despite the great effort to develop an effective vaccine against tuberculosis (TB) there is currently no reliable and safe human challenge model that can be used for in vivo evaluation of new TB vaccine candidates and/or elucidation of the mechanisms of TB protective immunity. In this study, five volunteers were challenged with BCG intradermally (ID). Swab specimens were collected at multiple time points from the vaccination site pre- and post-vaccination to quantitate mycobacterial shedding as a surrogate of in vivo mycobacterial immunity. We compared the performance of the TaqMan qPCR assay against colony-forming unit cultures on 7H10 agar plates, and time to positivity (TTP) of mycobacterial growth indicator tubes (MGIT) in order to evaluate the reproducibility and sensitivity in measuring BCG burden in swab specimens. BCG was detected in swab specimens from all five volunteers by at least one method, and no single method was superior in terms of sensitivity and reproducibility. A comparison of all three methods showed significant correlations by Spearman's rank test between 7H10 agar plating and qPCR (R = 0.601, P = 0.00072), MGIT culture TTP and 7H10 agar plating (R = 0.412, P = 0.029) as well as MGIT culture TTP and qPCR (R = −0.708, P = 0.00003). However, the three methods were somewhat different with regard to early versus late detection of BCG shedding post-challenge. This ID BCG challenge model has unique potential to further explore correlations between reactogenicity and immune mechanisms involved in protection against mycobacterial infections, and could therefore become a reliable tool in the evaluation process of new TB vaccination strategies.