Some previously immunodeficient HIV patients responding to antiretroviral therapy display poor recovery of CD4⁺ T cells. Evaluation of the contribution of thymic function requires sensitive detection and quantitation of metabolically active thymic tissue. We describe patients with low but detectable thymopoiesis assessed as circulating CD4⁺ naive T cells expressing CD31. High-resolution computed tomography and PET scans found no residual thymic tissue even though metabolic activity was demonstrable by PET in lymph nodes.