Reconstruction of HIV transmission links allows to trace the spread and dynamics of infection and guide epidemiological interventions. The aim of this study was to characterize transmission networks among subtype B infected patients from Poland. Maximum likelihood phylogenenetic trees were inferred from 966 HIV-1 subtype B protease/reverse transcriptase sequences from patients followed up in nine Polish HIV centers. Monophyletic clusters were identified using 3% within-cluster distance and 0.9 bootstrap values. Interregional links for the clusters were investigated and time from infection to onward transmission estimated using Bayesian dated MCMC phylogeny. Three hundred twenty one (33.2%) sequences formed 109 clusters, including ten clusters of ≥5 sequences (n = 81, 8.4%). Transmission networks were more common among MSM (234 sequences, 68.6%) compared to other infection routes (injection drug use: 28 (8.2%) and heterosexual transmissions: 59 (17.3%) cases, respectively OR:3.5 (95%CI:2.6-4.6),p<0.001. Frequency of clustering increased from 26.92% in 2009 to 50.6% in 2014 OR:1.18 (95%CI:1.06-1.31),p = 0.0026; slope +2.8%/year with median time to onward transmission within clusters of 1.38 (IQR:0.59-2.52) years. In multivariate models clustering was associated with both MSM transmission route OR:2.24 (95%CI:1.38-3.65),p<0.001 and asymptomatic stage of HIV infection OR:1.93 (95%CI:1.4-2.64),p<0.0001. Additionally, interregional networks were linked to MSM transmissions OR:4.7 (95%CI:2.55-8.96),p<0.001. Reconstruction of the HIV-1 subtype B transmission patterns reveals increasing degree of clustering and existence of interregional networks among Polish MSM. Dated phylogeny confirms the association between onward transmission and recent infections. High transmission dynamics among Polish MSM emphasizes the necessity for active testing and early treatment in this group.