To investigate the endocrine responses to five different doses of FE 999049, a novel recombinant FSH derived from a human cell-line (PER.C6) during controlled ovarian stimulation in a GnRH antagonist cycle, and to characterize them according to serum AMH. Exploratory analysis of 222 IVF/ICSI patients undergoing controlled ovarian stimulation with FE 999049 (Ferring Pharmaceuticals) in a randomized, assessor-blind, multicentre, dose-response trial (NCT01426386). Patients were randomized to fixed doses of 5.2, 6.9, 8.6, 10.3 or 12.1 μg/day FE 999049. Randomization was stratified by serum AMH (low: 5.0-14.9 pmol/L, high: 15.0-44.9 pmol/L; Beckmann-Coulter Gen 2 ELISA). Stimulation was carried out in a GnRH antagonist cycle (ganirelix 0.25 mg/day from day 6). Blood was sampled at stimulation days 1, 4 and 6 and end-of-stimulation for central analysis. Ongoing pregnancy was determined 10-11 weeks after compulsory single blastocyst transfer. Serum estradiol, inhibin B and inhibin A on days 4, 6 and end-of-stimulation were positively associated with FE 999049 dose in both AMH strata (p<0.05). Serum progesterone on day 6 and end-of-stimulation was positively correlated with FE 999049 dose only in the high AMH stratum (p<0.01). Progesterone levels ≥1 ng/mL during stimulation were associated with a reduced ongoing pregnancy rate in the low AMH stratum (p<0.01), but had no impact in the high AMH stratum. The percentage of patients with premature LH rise (≥10 IU/L) increased with FE 999049 dose (p<0.01), and was associated with a reduced ongoing pregnancy rate (p<0.05) independent of AMH. Serum estradiol, progesterone, inhibin A and inhibin B are significantly correlated with the dose of FE 999049. Both premature LH rise and elevation of progesterone seem to be associated with a reduced ongoing pregnancy rate. The negative impact of elevated progesterone on treatment outcome is observed in patients with low AMH levels.