The immunosuppressive drugs rapamycin and cyclosporin A (CsA) are widely used to prevent allograft rejection. Moreover, they were shown to be instrumental in experimental models of tolerance induction. However, it remains to be elucidated whether these drugs have an effect on the CD4⁺CD25⁺ regulatory T-cell (T_REG) population, which plays an important role in allograft tolerance. Recently, we reported that alloantigen-driven expansion of human CD4⁺CD25⁺ T_REGs gives rise to a distinct highly suppressive CD27⁺T_REG subset next to a moderately suppressive CD27^-T_REG subset. In the current study we found that rapamycin and CsA do not interfere with the suppressive activity of human naturally occurring CD4⁺CD25⁺ T cells. However, in contrast to CsA, rapamycin preserved the dominance of the potent CD27⁺T_REG subset over the CD27^-T_REG subset after alloantigen-driven expansion of CD4⁺CD25⁺ T_REGs in vitro. Accordingly, CD4⁺CD25⁺ T_REGs cultured in the presence of rapamycin displayed much stronger suppressive capacity than CD4⁺CD25⁺ T_REGs cultured in the presence of CsA. In addition, CD4⁺CD25⁺ T_REG cells cultured in the presence of rapamycin, but not CsA, were able to suppress ongoing alloimmune responses. This differential effect of rapamycin and CsA on the CD27⁺T_REG subset dominance may favor the use of rapamycin in tolerance-inducing strategies.