The goal of this study was to define, by surgical removal of the thymus in juvenile rhesus macaques, the role of the thymus in peripheral T cell homeostasis and to assess the significance of thymic output in SIV infection. By monitoring the changes in phenotypic T cell markers as well as in the numbers of TCR excisional circles--a recently described marker for recent thymic emigrants--following thymectomy, we present evidence that surgical thymectomy in juvenile macaques results in a faster decay of peripheral CD4(+) cells, but does not cause a substantial shift in CD45RA(+) and CD45RA(-) populations. We were able to measure a thymic output of 0.32% and 0.21% per day of CD4(+) and CD8(+) cells, respectively. No compensatory extra-thymic source was detected in lymphoid tissues, although there was a small compensatory increase in T cell proliferation in the peripheral T cell pool. After SIV infection, thymectomized animals did not have higher viral loads, greater T cell decay, or faster disease progression. We therefore conclude that peripheral destructive processes, rather than a loss of thymic output, appear to be the main causes of T cell depletion in SIV infection.