Tuberculosis (TB) is a notifiable disease in Denmark. Underreporting leads to underestimation of the disease burden and may impede disease control. To date, no other published studies have examined underreporting of TB in the Danish setting. Records of patients in the Region of Southern Denmark diagnosed with TB from 2009 to 2014 in the Danish National Patient Registry (DNPR) were linked to the national notification database. Medical records of non-notified patients were reviewed, followed by statistical comparison of demographic and medical parameters with notified TB patients in the region. In the study period, 28.9% (=30) of clinically diagnosed, culture-negative TB cases were not notified, corresponding to an overall TB underreporting rate of 7.5%. Non-notified patients had fewer co-morbidities and were less likely to have had previous TB episodes. Incidentally, we found a high number (71.1%) of erroneous TB diagnoses in the DNPR. Accurate data based on notification is essential to understand possible needs for preventive actions in the population. Our study demonstrates the existence of underreporting of culture-negative TB cases in the Region of Southern Denmark.