One of the strategies that has been investigated to reduce antiretroviral treatment toxicity in patients infected with human immunodeficiency virus (HIV) is structured treatment interruption (STI). Our aim was to analyze early viral and immune dynamics after interruption of highly active antiretroviral therapy (HAART) and to determine whether thymic function-related markers play a role in preventing CD4 count decline caused by increased viral replication. This was a prospective study of an open cohort of 47 HIV-infected patients with a median 969 CD4 count and prolonged viral suppression. They were followed every 4 weeks though week 24. Thymic volume and TREC level were analyzed at baseline. Increased thymic volume was associated with higher plasma viral load and greater CD4 count decline early after interruption. Three virologic patterns were observed: rapid/high (RH), delayed/high (DH), and low/slow (LS) viral replication. RH correlated with higher thymic volume at baseline and with higher CD4 count decline at week 4. Patients with greater thymic volume was associated with an immune and virologic impairment only early after interruption, probably because of infection of the increased number of available target cells. As the long-term consequences of these observations are unknown, the safety of treatment interruption must be further studied.