| Q50 | Congenital malformations of ovaries, fallopian tubes and broad ligaments |
| Q50.0 | Congenital absence of ovary |
| Q50.01 | Congenital absence of ovary, unilateral |
| Q50.02 | Congenital absence of ovary, bilateral |
| Q50.1 | Developmental ovarian cyst |
| Q50.2 | Congenital torsion of ovary |
| Q50.3 | Other congenital malformations of ovary |
| Q50.31 | Accessory ovary |
| Q50.32 | Ovarian streak |
| Q50.39 | Other congenital malformation of ovary |
| Q50.4 | Embryonic cyst of fallopian tube |
| Q50.5 | Embryonic cyst of broad ligament |
| Q50.6 | Other congenital malformations of fallopian tube and broad ligament |
| Q51 | Congenital malformations of uterus and cervix |
| Q51.0 | Agenesis and aplasia of uterus |
| Q51.1 | Doubling of uterus with doubling of cervix and vagina |
| Q51.10 | Doubling of uterus with doubling of cervix and vagina without obstruction |
| Q51.11 | Doubling of uterus with doubling of cervix and vagina with obstruction |
| Q51.2 | Other doubling of uterus |
| Q51.3 | Bicornate uterus |
| Q51.4 | Unicornate uterus |
| Q51.5 | Agenesis and aplasia of cervix |
| Q51.6 | Embryonic cyst of cervix |
| Q51.7 | Congenital fistulae between uterus and digestive and urinary tracts |
| Q51.8 | Other congenital malformations of uterus and cervix |
| Q51.81 | Other congenital malformations of uterus |
| Q51.810 | Arcuate uterus |
| Q51.811 | Hypoplasia of uterus |
| Q51.818 | Other congenital malformations of uterus |
| Q51.82 | Other congenital malformations of cervix |
| Q51.820 | Cervical duplication |
| Q51.821 | Hypoplasia of cervix |
| Q51.828 | Other congenital malformations of cervix |
| Q51.9 | Congenital malformation of uterus and cervix, unspecified |
| Q52 | Other congenital malformations of female genitalia |
| Q52.0 | Congenital absence of vagina |
| Q52.1 | Doubling of vagina |
| Q52.10 | Doubling of vagina, unspecified |
| Q52.11 | Transverse vaginal septum |
| Q52.12 | Longitudinal vaginal septum |
| Q52.2 | Congenital rectovaginal fistula |
| Q52.3 | Imperforate hymen |
| Q52.4 | Other congenital malformations of vagina |
| Q52.5 | Fusion of labia |
| Q52.6 | Congenital malformation of clitoris |
| Q52.7 | Other and unspecified congenital malformations of vulva |
| Q52.70 | Unspecified congenital malformations of vulva |
| Q52.71 | Congenital absence of vulva |
| Q52.79 | Other congenital malformations of vulva |
| Q52.8 | Other specified congenital malformations of female genitalia |
| Q52.9 | Congenital malformation of female genitalia, unspecified |
| Q53 | Undescended and ectopic testicle |
| Q53.0 | Ectopic testis |
| Q53.00 | Ectopic testis, unspecified |
| Q53.01 | Ectopic testis, unilateral |
| Q53.02 | Ectopic testes, bilateral |
| Q53.1 | Undescended testicle, unilateral |
| Q53.10 | Unspecified undescended testicle, unilateral |
| Q53.11 | Abdominal testis, unilateral |
| Q53.12 | Ectopic perineal testis, unilateral |
| Q53.2 | Undescended testicle, bilateral |
| Q53.20 | Undescended testicle, unspecified, bilateral |
| Q53.21 | Abdominal testis, bilateral |
| Q53.22 | Ectopic perineal testis, bilateral |
| Q53.9 | Undescended testicle, unspecified |
| Q54 | Hypospadias |
| Q54.0 | Hypospadias, balanic |
| Q54.1 | Hypospadias, penile |
| Q54.2 | Hypospadias, penoscrotal |
| Q54.3 | Hypospadias, perineal |
| Q54.4 | Congenital chordee |
| Q54.8 | Other hypospadias |
| Q54.9 | Hypospadias, unspecified |
| Q55 | Other congenital malformations of male genital organs |
| Q55.0 | Absence and aplasia of testis |
| Q55.1 | Hypoplasia of testis and scrotum |
| Q55.2 | Other and unspecified congenital malformations of testis and scrotum |
| Q55.20 | Unspecified congenital malformations of testis and scrotum |
| Q55.21 | Polyorchism |
| Q55.22 | Retractile testis |
| Q55.23 | Scrotal transposition |
| Q55.29 | Other congenital malformations of testis and scrotum |
| Q55.3 | Atresia of vas deferens |
| Q55.4 | Other congenital malformations of vas deferens, epididymis, seminal vesicles and prostate |
| Q55.5 | Congenital absence and aplasia of penis |
| Q55.6 | Other congenital malformations of penis |
| Q55.61 | Curvature of penis (lateral) |
| Q55.62 | Hypoplasia of penis |
| Q55.63 | Congenital torsion of penis |
| Q55.64 | Hidden penis |
| Q55.69 | Other congenital malformation of penis |
| Q55.7 | Congenital vasocutaneous fistula |
| Q55.8 | Other specified congenital malformations of male genital organs |
| Q55.9 | Congenital malformation of male genital organ, unspecified |
| Q56 | Indeterminate sex and pseudohermaphroditism |
| Q56.0 | Hermaphroditism, not elsewhere classified |
| Q56.1 | Male pseudohermaphroditism, not elsewhere classified |
| Q56.2 | Female pseudohermaphroditism, not elsewhere classified |
| Q56.3 | Pseudohermaphroditism, unspecified |
| Q56.4 | Indeterminate sex, unspecified |