AimThe aim of this study was to assist clinicians evaluating refugee children for latent tuberculosis infection (LTBI) by comparing paired tuberculin skin test (TST) and Quantiferon Gold In‐Tube (QGIT) test results with clinical management decisions and follow‐up data in a large cohort of newly arrived refugee children.MethodsThis was a retrospective analysis of all refugee children (<15 years of age) evaluated for LTBI with both TST and interferon‐γ release assay between 2007 and 2010 in the Illawarra‐Shoalhaven region of New South Wales, Australia. Demographics, country of origin, bacille Calmette–Guerin (BCG) vaccination status, chest X‐ray results, TST and QGIT test results, clinical management and outcome on long‐term follow‐up were assessed.ResultsOf 272 children evaluated, complete results were available for 212 (78%). The vast majority (207; 98%) were from Africa or Southeast Asia. Overall, 33 (16%) children were treated for LTBI; 13 (39%) had concordant TST and QGIT results and 20 (61%) discordant results. Of 63 (30%) TST‐positive (≥10 mm) children, 46 (73%) were QGIT assay‐negative, 44 (70%) had a BCG scar, 3 (5%) were younger than 2 years and 6 (10%) were treated for LTBI. Of 32 QGIT assay‐positive children, 15 (47%) were TST negative, 31 (97%) had a BCG scar, all were older than 2 years and 14 (44%) were treated for LTBI.ConclusionsDiscordant TST and QGIT results were found in a high percentage of refugee children. QGIT is convenient and more specific than TST to diagnose LTBI in BCG‐vaccinated children, although a careful tuberculosis exposure history and clinical assessment to rule out active disease remain important.