Gene therapy has the potential to maintain therapeutic blood clotting factor IX (FIX) levels in patients with hemophilia B by delivering a functional human F9 gene into liver cells. This phase 1/2, open-label dose-escalation study investigated BAX 335 (AskBio009, AAV8.sc-TTR-FIXR338Lopt), an adeno-associated virus (AAV) serotype 8-based FIX Padua gene therapy, in patients with hemophilia B. This report focuses on 12-month interim analyses of safety, pharmacokinetics, effects on FIX activity, and immune responses for dosed participants. Eight adult males (aged 20-69 years; range FIX activity, 0.5%-2.0%) received 1 of 3 BAX 335 IV doses: 2.0 × 1011; 1.0 × 1012; or 3.0 × 1012 vector genomes/kg. Three (37.5%) participants had 4 serious adverse events (SAEs), all considered unrelated to BAX 335. No SAE led to death. No clinical thrombosis, inhibitors, or other FIX Padua-directed immunity were reported. FIX expression was measurable in 7 of 8 participants; peak FIX activity displayed dose dependence (32.0%-58.5% in cohort 3). One participant achieved sustained therapeutic FIX activity of ~20%, without bleeding or replacement therapy, for 4 years; in others, FIX activity was not sustained beyond 5-11 weeks. In contrast to some previous studies, corticosteroid treatment did not stabilize FIX activity loss. We hypothesize that the loss of transgene expression could have been caused by stimulation of innate immune responses including CpG oligodeoxynucleotides introduced into the BAX 335 coding sequence by codon optimization. Registered at www.clinicaltrials.gov as NCT01687608.