Many of the presenting features in women with Cushing's syndrome (CS) are similar to those observed for patients with polycystic ovary syndrome (PCOS). The aim of this study was to compare gonadotropin pulsatility characteristics in CS and PCOS. We evaluated 32 females divided into three groups. The first group comprised 12 females with clinically and biochemically proven CS, subsequently confirmed by histology (seven with Cushing's syndrome, five with adrenal adenoma). The second group comprised ten females with clinical, endocrine and ultrasonographic parameters for PCOS, while the third group comprised ten healthy females with regular menstrual cycles to serve as controls. Blood samples were taken at 15-min intervals for 6 h in the follicular phase, for determination of luteinizing hormone (LH) and follicle-stimulation hormone (FSH). Pulse analysis was carried out using the PulsDetekt program, and statistical analysis was done using the Kruskal-Wallis test. The following data, presented as median (minimum-maximum), were found for the three groups respectively. Number of LH pulses: 0 (0-5), 7 (3-8) and 3 (2-7); LH pulse amplitude: 2.29 (1.98-3.49), 2.27 (1.15-5.90) and 2.03 (1.02-4.46) mU/l; LH pulse mass: 17.81 (14.82-26.20), 29.85 (8.59-185.82) and 27.57 (7.63-66.69) mU/l x min. Number of FSH pulses: 3 (0-3), 2 (0-5) and 3 (1-5); FSH pulse amplitude: 1.62 (1.29-1.94), 1.49 (1.19-4.40) and 2.02 (1.37-2.52) mU/l; FSH pulse mass: 12.17 (9.64-41.69), 11.18 (8.92-33.02) and 15.16 (10.31-18.93) mU/l x min. Only the number of pulses was compared because other parameters of pulsatile secretion cannot be estimated when no pulses are detected. The difference in number of LH pulses between groups was statistically significant (p < 0.05); however, there was no difference in the number of detected FSH pulses between groups (p > 0.05). Attenuation of pulsatile LH secretion indicating gonadotropin deficiency in the majority of women with CS is mostly due to alterations in serum cortisol levels. Our data also suggest that different mechanisms alter LH pulsatile secretion in CS and PCOS.