Fifty-six of 182 (31%) children had indeterminate QuantiFERON assays. Indeterminate assays were associated with inpatient status [odds ratios (OR): 11.7, 95% confidence interval 3.9-34.9], but not with age, gender or medical comorbidities. This indicates that indeterminates may be due to specimen handling, and proper procedural training may be necessary to decrease indeterminate QuantiFERON results.