The Xpert(®) MTB/RIF assay has demonstrated robust capability for diagnosing tuberculosis (TB) and rifampin (RMP) resistance. Optimal use of Xpert in diverse settings will require knowledge of challenges when interpreting the results. We present three selected cases from the United States, a low-burden TB setting, to highlight important clinical scenarios encountered with Xpert testing: rapid RMP resistance detection in a patient with pre-extensively drug-resistant TB who immigrated from the Philippines, false-positive RMP resistance detection, and Mycobacterium tuberculosis detection in a culture-negative patient. These cases demonstrate that a low pre-test probability of TB or drug-resistant TB can complicate the interpretation of the Xpert assay.