The purpose of this prospective, cross-sectional observational study was to compare the tuberculin skin testing (TST) with QuantiFERON-TB Gold-In Tube (QTF-GIT) for the detection of latent tuberculosis infection in healthcare workers (HCWs). The study included 78 volunteers who are HCWs at the same tertiary care teaching hospital for chest diseases and tuberculosis. Participants with active tuberculosis, immunodefficiency or malnutrition were not included. The TST was administered by the Mantoux method. Peptides representing ESAT-6, CFP-10 and TB7-7 were used as TB-specific antigens in the whole-blood Interferon-gamma (IFN-g) assay (QTF-GIT). There was a statistically significant relation between the number of Bacillus Calmette-Guerin (BCG) scars and the diameter of TST (p< 0.01). QTF results according to previous BCG vaccinations did not significantly differ (p> 0.05). There was an intermediate concordance between two tests (k: 0.346). QTF-GIT has a sensitivity of 56.14% (both TST and QTF-GIT are positive), specificity of 90.48% (both TST and QTF-GIT are negative); positive predictive value of 94.12% and negative predictive value of 43.18% and accuracy is 65.38%. There was a statistically significant relation between TST diameter and QTF result (p< 0.01). Latent tuberculosis infection prevalance of our study population was 43% according to QTF-GIT test, 73% according to TST and BCG vaccination rate was 87%. In conclusion, TST is affected by previous BCG vaccinations, QTF-GIT is not. We can recommend QTF-GIT test for the detection of latent tuberculosis infection as an alternative to TST in populations with routine BCG vaccination programme.