Tuberculosis is a global healthcare challenge. Host genetic factors were proven to modify risk of the disease. Genome-wide association studies revealed a number of loci associated with TB in different populations. However, no systematic analysis of genetic bases of susceptibility to different clinical stages, such as primary TB and reactivation, was carried out. We set out to validate the results of GWASs in Russians of West Siberia with a consideration of primary and secondary TB. We chose 45 SNP from five large GWASs and genotyped 445 healthy individuals and 323 TB patients including 74 with primary TB and 249 with reactivation. We found that the rs7821565 and rs40363 SNPs were associated with primary TB in Russians (p = 0.019 and 1.4e−3, respectively), while rs10515787 and rs2837857 were associated with secondary TB (p = 1.2e−3 and 0.039, respectively). The results suggest genetic basis of primary and secondary TB differs.