Studies of the effects of estrogen replacement therapy on coronary heart disease risk have produced conflicting results. We hypothesize that this may be explained by differences in the length of estrogen deficiency prior to initiation of treatment and associated variation in plaque inflammation or stage of progression. The goal of this study was to determine whether estrogen administered after a period of deficiency affects plaque progression and leukocyte populations. Ovariectomized ApoE-/- mice were treated as follows: group 1: continuous estrogen for 90 days (E+/+); group 2: placebo for 45 days followed by estrogen for 45 days (E-/+); group 3: estrogen for 45 days followed by placebo for 45 days (E+/-); and group 4: placebo for 90 days (E-/-). Serum lipoprotein concentrations, plaque size and inflammatory cell (macrophage, CD3+, CD4+, CD8+, dendritic cell, and NK cell) densities were quantified. Plaque size was smaller in groups receiving early estrogen therapy. CD3+ and total inflammatory cell densities were lower in late estrogen therapy groups. The CD8 to dendritic cell ratio was significantly lower in the E-/+ group only. These results suggest that a period of estrogen deficiency followed by reintroduction alters the immunologic environment of atherosclerotic lesions as well as plaque progression.