Although antiretroviral therapy (ART) suppresses viral replication to clinically undetectable levels, HIV-1 persists in CD4+ T cells in a latent form not targeted by the immune system or ART1-5. This latent reservoir is a major barrier to cure. Many patients initiate ART during chronic infection, and in this setting, most proviruses are defective6. However, the dynamics of the accumulation and persistence of defective proviruses during acute HIV infection are largely unknown. Here we show that defective proviruses accumulate rapidly within the first few weeks of infection to make up over 93% of all proviruses in treated patients, regardless of how early ART is initiated. Using an unbiased screening method to amplify near full-length proviral gen omes from HIV-1 infected adults treated at different stages of infection, we demonstrate that early ART initiation limits the size of the reservoir but does not profoundly impact its composition. This analysis allows us to revise our understanding of the composition of the reservoir and estimate the true reservoir size in individuals treated early vs. late in infection. Additionally, we demonstrate that commonly used assays for measuring the reservoir do not correlate with reservoir size. These findings reveal hurdles that must be overcome to successfully analyze future HIV-1 cure strategies.