The aim of this study was to elucidate the etiology and clinical features of Taiwanese girls with isosexual precocious puberty. 460 girls with precocious puberty were enrolled in this study. 284 of them had a GnRH test and 179 girls with gonadotropin-dependent precocious puberty (GDPP) underwent brain MRI. Our results showed 7% of these 460 girls had gonadotropin-independent precocious puberty (GIPP). The other 93% patients had GDPP and 96% of them were idiopathic. Functional ovarian cyst and hypothalamic hamartoma were leading causes of GIPP and organic GDPP, respectively. The presence of undetectable basal serum FSH and LH levels had a specificity of 95% in girls with GIPP. Among girls with GDPP, those aged < 5 years had a higher percentage of detected CNS lesions than older girls (8% vs 3%). Girls with organic CNS lesions also had more advanced bone age SDS (6.9 +/- 3.3 vs 3.3 +/- 1.9), larger uterine volume (13.8 +/- 12.1 vs 6.6 +/- 8.1 cm3), higher basal serum estradiol (33.5 +/- 17.1 vs 26.8 +/- 18.2 pg/ml), and higher peak LH level after GnRH stimulation (45.2 +/- 36.2 vs 25.8 +/- 27.3 U/l) than those with idiopathic GDPP. In conclusion, GIPP is uncommon in Taiwanese girls with precocious puberty. Functional ovarian cyst and hypothalamic hamartoma are leading causes of GIPP and organic GDPP, respectively. The presence of neurological deficit, younger age at onset of puberty, presence of menstruation, rapid advance of bone age, markedly enlarged uterus, high serum estradiol, and high peak LH level after GnRH stimulation are suggestive of organic GDPP.