Tuberculin skin test (TST) and ELISPOT/T. SPOT.TB are two techniques frequently used to detect latent tuberculosis infection (LTBI), but doubts remain about their accuracy. The efficacy of these tests for detecting LTBI was the focus of an observational prospective longitudinal study in 24 patients with juvenile idiopathic arthritis receiving methotrexate therapy. Patients underwent both tests and were clinically and epidemiologically assessed for LTBI at baseline and after 3 and 12 months. Immunosuppressive therapy doubled the prevalence of LTBI (20.8% at baseline vs 41.6% at end of study) and epidemiological history was an important factor (relative risk 2.0). However, despite agreement between the tests being low at both 3 and 12 months, no evidence of superiority of one test over the other was observed, and in only one patient with positive T. SPOT.TB was the test useful in early detection of LTBI.