Objective: Isolated gonadotropin-releasing hormone(GnRH)deficiency(IGD)is a rare clinical condition with a broad spectrum of human reproductive disorders which varies from congenital isolated hypogonadotropic hypogonadism(IHH)to constitutional delay of puberty(CDP)and adult-onset isolated hypogonadotropic hypogonadism(AHH)in male.In the presence of anosmia or hyposmia,IHH is defined as Kallmann syndrome(KS),whereas in the presence of a normal sense of smell,it is termed normosmic IHH(nIHH).In this study,we described the clinical features of 213 Chinese IGD males,and performed genetic study in some of these cases,and analyzed their genotype phenotype correlations.Methods: We collected the male isolated GnRH deficiency patients in our outpatient and filed their medical and family history.The physical examinations,laboratory and imaging studies were performed.The PCR and agarose gel electrophoresis,whole genome chip and semiconductor target areas sequencing were used to reveal the molecular defects of two KS and ichthyosis brothers.We also used semiconductor target areas sequencing and Sanger sequencing to detect the mutations in 15 IHH causative genes in 4 KS patients with cleft lip/palate(CLP)and 8 IGD patients(including 5 KS patients,one nIHH patients and two AIHH patients)without CLP.Functional prediction and conservation analysis were performed to predict the consequence of the three mutations.Results: The reproductive phenotypes in the IHH patients included Gynecomastia(23/210),microphallus(42/210),cryptorchidism(21/210),unilateral testicular agenesis(2/210),scrotum dysplasia(3/210).The non-reproductive phenotypes in our patients contained ichthyosis(3/210),unilateral renal agenesis(2/210),cleft lip(2/210),cleft lip and dental agenesis(1/210),cleft lip and palate combined with dental agenesis and high arched palate(1/210),nystagmus and iris hypoplasia(1/2 10).These nonreproductive phenotypes only presented in KS patients.The results of karyotype analysis showed that 15 out of the 210 IHH patients(7.1%)had polymorphic chromosomal variants..The phenotypes of the two Chinese brothers with KS and X-linked ichthyosis were characterised by bilateral cryptorchidism,unilateral renal agenesis in one patient but normal kidney development in another.Genetic study showed that the two affected siblings had the same novel deletion at Xp22.3 including exons 9-14 of KAL1 gene and entire STS gene.We also identified two novel heterozygous missense mutations in FGFR1,(NM_001174066):c.776G>A(p.G259E)and(NM_001174066): c.358C>T(p.R120C),in a 23-yr-old KS male with cleft lip and an 18-year-old KS patient with cleft lip and palate,dental agenesis and high arched palate,respectively.By the way,one heterozygous missense mutation in KISS1R which was reported previously,(NM_032551): c.587C>A(p.P196H),was identified in an 18-yr-old KS male with cleft lip and dental agenesis.All the mutations were not presented in any of the 200 unrelated normal controls.However,we proved the KISS1R c.587C>A mutation was presented in the father and grandfather of the patients.Conclusions: Our study expanded the clinical phenotype and gene mutation spectrum of Chinese IGD patients and has implications for the genetic diagnoses and counseling of IGD.