Abstract: Objective To identify the origin and clinical significance of small supernumerary marker chromosome, and provide information for genetic counseling and treatment. Methods Chromosome karyotype of infertility and abnormal development patients admitted to Chinese PLA General Hospital from 2014 to 2015 were detected by G-binding technique, and fluorescence in situ hybridization technique and real-time PCR were performed to analyze the samples with small supernumerary marker chromosome. Results Three subjects were screened out from 2 386 genetic counseling subjects from 2014 to 2015 with small supernumerary marker chromosome:a 28 years old male patient with infertility, a 20 years old female patient with primary amenorrhea and a 6 years old male patient with growth retardation. The three small supernumerary marker chromosomes originated from chromosome 15, chromosome Y and chromosome X. Conclusion Small supernumerary marker chromosome can result in infertility, spontaneous abortion, amenorrhea, gonad dysplasia and so on, which can be clearly diagnosed using cytogenetic and molecular genetic techniques.