Objective To investigate whether chronic treatment with a GnRH-agonist influences follicular growth and morphology during the gonadotrophin-independent phase and if normal ovarian function is restored after discontinuing agonist treatment. Design Prospective study. Materials and Methods Cycling heifers were allocated to a control group (n=8) or a group that received a controlled-release GnRH-agonist implant (n=48). After 91 days, implants were removed and ovaries recovered (n=8) on Days 0, 3, 7, 14, 28 and 56 after removal. After collection of ovaries, all visible follicles were removed by dissection, measured, and prepared for histology. Follicles were classified as healthy or atretic based on morphological assessment. Parametric and non-parametric tests were used to test for differences in follicular features between heifer groups. Results Chronic treatment with GnRH agonist reduced (P<0.001) the occurrence of ovulation. There was no evidence of corpus luteum in ovaries from heifers on Days 0, 3, 7, 14 and 28 after the discontinuation of agonist treatment. Ovaries from heifers on Day 56 after treatment had a corpus luteum similar to controls. Controls had more (P=0.02) follicles than heifers on Day 0 after agonist treatment. For all follicles observed for controls (n=173) and heifers treated with agonist (n=274), there were no differences amongst groups in follicle size (P=0.47), healthy follicles (P=0.24) or atretic follicles (P=0.24). Conclusion Chronic treatment with the GnRH agonist, which suppresses FSH and LH and halts follicular waves, has no apparent effect on follicle growth or morphology during the gonadotrophins independent phase of follicle development. Ovaries suppressed long-term return to normal follicular growth and ovulation after the discontinuation of agonist treatment. The findings provide further support for the general understanding that follicular growth and development during the gonadotrophin-responsive phase can proceed essentially in the absence of significant FSH in circulation.