Complex endocrine relationships exist among the hypothalamus, pituitary, ovaries and thymus. There is also considerable evidence showing gonadotropin releasing hormone (GnRH) involvement in modulating immune system functions. The present study investigated the sequential changes in functional lymphocyte subsets in primary lymphoid tissues of prepubertal female mice in vivo following GnRH agonist treatment in slow release microcapsule formulation. A direct two color immunofluorescence staining followed by flow cytometry was employed. Single i.m injection of agonist significantly decreased both absolute and relative thymic weights and absolute thymocyte counts. No differences, however, were observed in the percentage of thymocytes expressing Thy 1.2, CD4 and CD8. Absolute levels of thymic T cells, CD8 positive cells, immature cells expressing both CD4 and CD8, and immature subsets differentiating toward CD4 were significantly reduced two weeks after agonist treatment. The percentage of bone marrow B cells was also significantly decreased at the second and third weeks following agonist administration. Functional studies to determine in vivo cell-mediated immune function also indicated a significant suppression following agonist administration. These data, together with our earlier observations on secondary lymphoid tissues, suggest a general suppression of lymphocyte maturation at an early stem cell stage of development in prepubertal female mice in vivo.