We compared the performance of two PCR assays, an IS6110-based in-house protocol and the COBAS AMPLICOR MTB PCR (COBAS MTB) system, for the detection of Mycobacterium tuberculosis complex in 43 human lymph node samples from 40 patients. For the in-house PCR and the COBAS MTB assays, respectively, sensitivities were 87.5% versus 45.5% (P < 0.05), specificities were 100.0% versus 91.3% (P > 0.05), and inhibition rates were 4.8% versus 19.5% (P < 0.05). For the COBAS MTB system, additional N-acetyl-L-cysteine-NaOH pretreatment of the samples changed neither the inhibition rate nor the sensitivity significantly.