Summary Although a vast majority of HIV-1 -positive patients in the UK are infected with clade B virus, a large number of newly diagnosed cases of heterosexually transmitted HIV-1 are acquired abroad, in countries where non-B clade HIV-1 predominates. Since the development of the viral load assay in 1988, assessment of HIV-1 plasma viraemia has become an integral part of HIV clinical care; however, the contemporary viral load assay was developed and optimized for clade B HIV-1. Here we report the underquantification of viraemia in an individual infected with clade A virus, and the consequent initial classification of the patient as an HIV controller (HIC). Immunological investigations of interferon (IFN)-γ and lymphoproliferative responses to HIV-1 clade B antigens and peptides, in parallel with mitogenic stimulation, were performed. Subsequent comparison with responses observed within clade B-infected HIC led to viral sequencing, confirmation of infecting clade and recommendation of antiretroviral therapy initiation. We emphasize the growing need for awareness of possible limitations of the commonly used viral load assays, which cannot be relied upon unreservedly in a clinical setting. Furthermore, this case highlights the increasing need for more detailed investigation into both viral genetics and fitness when defining patients as HIC.