Background: Pre-exposure prophylaxis (PrEP) with emtricitabine/tenofovir (TFV) disoproxil fumarate (FTC/TDF) is highly protective against HIV infection. We report a case of TDFsusceptible, FTC-resistant HIV acquisition despite high adherence to PrEP, confirmed by PrEP drug level testing. Methods: Adherence to FTC/TDF was assessed by measuring FTC/TFV levels or their metabolites in plasma, dried blood spots (DBS), and hair. Genotypic and phenotypic resistance of the acquired virus was evaluated by standard clinical tests and by single-genome sequencing (SGS) of > 50 proviruses obtained from peripheral blood mononuclear cells (PBMC). HIV partner services (PS) identified the likely transmission partner. Findings: A 21 year-old Latino man tested positive for HIV (negative HIV antibody, HIV RNA 559 copies per mL) 13 months after PrEP initiation. He reported excellent adherence to daily PrEP. He was linked to care and immediately started antiretroviral treatment (ART), at which point his RNA was 1544 copies per mL and his HIV Ab test was positive. The HIV genotype revealed M184V, L74V, L100I and K103N mutations in reverse transcriptase (RT); the phenotype showed susceptibility to TDF and resistance to FTC. FTC/TFV levels by liquid chromatography/tandemmass-spectrometry (LC-MS/MS) measured in 1 centimeter (cm) segments of hair from the scalp indicated consistently high PrEP adherence in each of the preceding six months. TFV-diphosphate and FTC-triphosphate levels in DBS indicated high adherence over the preceding six weeks. TFV and FTC levels measured in plasma ten weeks prior to HIV seroconversion confirmed adherence in the days preceding that visit. The likely transmission partner, named during PS, was not engaged in HIV primary care and the viral genotype was similar. Interpretation: Acquisition of TDF-susceptible, FTC-resistant HIV infection can occur despite high PrEP adherence. Quarterly HIV and STD screening of patients on PrEP, combined with prompt linkage to care and PS for those diagnosed with HIV, facilitates early diagnosis and prevents further transmission of HIV. Cohen et al.