The rate of low-mitogen indeterminate interferon-gamma release assay results at a hospital with expert pediatric phlebotomy and rapid incubation of specimens was 0.96%. All low-mitogen indeterminate results were found to be associated with an immunocompromised or anergic state. We describe a child where an unexpected indeterminate interferon-gamma release assay test pointed to an underlying anergic condition and was of diagnostic significance.