An acute challenge of exogenous GnRH elicits rapidly increased serum gonadotropin levels with qualitative changes to more basic isoforms of both FSH and LH. Chronic GnRH agonist therapy suppresses endogenous gonadotropins, and the serum levels of FSH and LH are low and fairly constant. A possible qualitative change in the gonadotropins during GnRH agonist therapy was investigated by determination of the median charge of the gonadotropin isoforms before and during therapy in 18 pubertal children. Two different GnRH agonists were studied: buserelin, given intranasally or as a sc implant for 1.5-34 months to five girls, aged 7-10 yr, and for 5-6 months to two boys, aged 11-13 yr; and triptorelin, administered as a depot preparation for 3-6 months to four girls, aged 9-12.5 yr, and for 1-24 months to seven boys, aged 10.5-12 yr. FSH and LH in serum and eluates after electrophoresis in 0.10% agarose suspension were measured with sandwich fluoroimmunoassays. The mean serum FSH and LH levels decreased significantly (P < 0.05) in girls during triptorelin therapy, whereas only the FSH level decreased (P < 0.05) in the boys. There were no significant (P > 0.05) changes in serum gonadotropin levels during buserelin therapy. All of the children had more basic serum isoforms of LH, and all but one had more basic forms of FSH during the GnRH agonist treatments. In a girl who had more basic gonadotropin isoforms after treatment with triptorelin for 2 and 6 months, a GnRH challenge elicited the release of still more basic isoforms. The changes in mean median charge to more basic gonadotropin isoforms were highly significant for both busereline (P < 0.01) and triptorelin (P < 0.001) treatment. An increased (P < 0.001) degree of charge heterogeneity was observed for FSH after triptorelin therapy. These findings show that there is a qualitative change in the isoforms of both FSH and LH in serum during GnRH agonist therapy in pubertal children. The changes in charge to more basic gonadotropin isoforms most likely reflect a direct effect at the pituitary level, leading to the synthesis and/or selective release of less sialylated and sulfated isoforms of the gonadotropins. The observed qualitative changes in the gonadotropin isoforms in these pubertal children may be part of the clinical effects of GnRH agonist therapy, leading to an arrest or regression of puberty.