In craniates from hagfish to humans, the stem cells known as spermatogonia and oogonia which will produce the gametes later in life do not form in the gonads.  Instead, they are produced in yolk sac and must subsequently migrate to the gonads (Romer, p. 421).  The primordial germ cells form in the yolk sac (near the allantois) in the 5th week of embryonic development and they migrate towards the genital ridge, which forms in the 6th week of embryonic development.  If they do not reach this ridge, gonads do not form (Sadler, p. 271). These primordial germ cells (PCGs) are capable or forming spermatogonia or oogonia, depending on the environment in which migrate (Tilmann, 2002). 
germ cells

     Although some structures of the reproductive system may be single structures as adults, it should be remembered that in embryos they develop as paired structures (similar to the condition found in lower vertebrates). Some males are born with the condition of hemipenis and hemiscrotum (Moore, p.  320), double penises (from two embryonic genital tubercles), or a forked penis (from a branched genital tubercle) (Jones, 1991). In the case of the uterus, for example, it is paired in some mammals, a single fused structure in others, and fused at the base but with separate branches leading to the two oviducts in others.  In the human embryo, the uterus begins as a pair of uterine tubes which begin their fusion caudally (Sadler, p. 282).  The condition known as uterus didelphys occurs if the two female tubes fail to fuse producing a double vagina and uterus.  The condition known as uterus bicornis results from incomplete fusion.  A septum may persist in the uterus and the cervix may be double. Conditions such as these exist in about one in every 1500 female births (Jones, 1991; Jarcho, Julius).  HOXA13 mutations cause the formation of a bicornuate uterus (Manouvrier-Hanu, 1999). 

  Although adult humans do not possess a cloaca, the tissues derived from the embryonic cloacal folds do form part of the reproductive system.  The cloacal folds form the urogenital folds (which form the penis in males and the labia minora in females) and anal folds.  In males with hypospadias, there are abnormal uretral openings because the fusion of the folds was not complete (Sadler, p. 283-4).
     In both males and females, the gonads develop high in the abdomen, superior to the metanephric kidneys.  From this original position, they must descend to the pelvic brim (in females) or outside the abdomenopelvic cavity into the scrotum (in males).  As a result of this descent, males have an opening in the body wall, the inguinal canal, through which the testes pass which is the site where the components of the spermatic cord (vas deferens, testicular blood vessels, nerves) enter the body.  This condition leaves males susceptible to inguinal hernias.  Some male infants suffer from congenital inguinal hernia (Moore, p.  343).   (The inguinal canal in the human model is depicted in the adjacent photo).  
     In cryptorchism, one or both of the testes do not descend into the scrotum in infant males.  Because of the high internal body temperature, a testis maintained within the body will be unable to produce mature sperm. About 30% of premature males and 3-4% of full term males suffer from undescended testes.  Other male infants have ectopic testes which pass through the inguinal canal but do not reach the scrotum.  A testis can even migrate into the penis (Concodora, 1976; (Moore, p.  343).  abnormal

     In most females, the mesonephros and its ducts degenerate completely and the reproductive system is completely separate from the urinary system.  In males however, mesonephric ducts are retained but as parts of the reproductive tract rather than the urinary tract.  Both semen and urine pass through the urethra and therefore, the urinary and reproductive systems are not completely separate.  Females may have remnants of the mesonephros which form structures known as the appendix vesiculosa, epoophoron, paraphoron, and duct of Gartner.  In males, persistent mesonephric tissue may form the appendix of the testes (Moore, p.  333). 

     Some fetuses suffer from the absence of the clitoris or penis (Moore, p.  338) or the absence of the vagina (Moore, p.  339). The absence of the clitoris is a rare congenital abnormality. It is sometimes observed with other abnormalities, such as the absence of the labia minora or majora (Bellemare, 2005). Some females are born with an extra ovary (Cruikshank, 1990). Male abnormalities can include the absence of the penis, a micropenis (caused by lack of pituitary secretion) (Jones, 1991).

True hermaphrodites may posses one ovary and one testis (with male ducts on one side and female ducts on the other) or a gonad called an ovotestis which possesses both male and female cells (and may possess a combination of male and female duts). Pseudohermaphrodites possess genetalia which correspond to the opposite gender of that represented by the gonads (Jones, 1991).

Several polar bears are known to have had enlarged an clitoris; some were misidentified as pseudohermaphrodites (Sonne, 2005).