Objectives: To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. Methods: The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of > 2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list. Results: The majority (75.6%) were infected with subtype B and 6.6% with rare complex or unique recombinant forms. At a mutation frequency threshold of > 20%, 7.2% (95% CI 5.0%-10.1%) of the sequences had TDR and this doubled to 15.8% (95% CI 12.6%-19.6%) at > 2% mutation frequency (P < 0.0001). The majority (26/42, 62%) of low-frequency variants were against PIs. The most common mutations detected at > 20% and 2%- 20% mutation frequency differed for each drug class, these respectively being: L90M (n=7) and M46IL (n=10) for PIs; T215rev (n=9) and D67GN (n=4) for NRTIs; and K103N (n=5) and G190E (n=2) for NNRTIs. Combined TDR was more frequent in subtype B than non-B (OR=0.38; 95% CI=0.17-0.88; P=0.024) and had minimal predicted effect on recommended first-line therapies. Conclusions: The data suggest differences in the types of low-frequency compared with majority TDR variants that require a better understanding of the origins and clinical significance of low-frequency variants. This will better inform diagnostic and treatment strategies.