Objectives: To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. Methods: TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012–2013 and 2014–2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit–variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012–2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014–2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases. Results: The average annual rate of change in TB incidence for native Danes was −2.4% vs. −6.1% and −6.9% for native Swedes and Finns respectively. In 2012–2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014–2015, a similar pattern was seen. Conclusions: The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries.