Severe prenatal deficiency of GH, as occurs in congenital hypopituitarism, has little effect on fetal growth. However, prenatal and congenital deficiency can reduce the size of a male's penis, especially when gonadotropins are also deficient. Besides micropenis in males, additional consequences of severe deficiency in the first days of life can include hypoglycemia and exaggerated jaundice (both direct and indirect hyperbilirubinemia).

Even congenital GH deficiency does not usually impair length growth until after the first few months of life. From late in the first year until mid teens, poor growth and/or shortness is the hallmark of childhood GH deficiency. Growth is not as severely affected in GH deficiency as in untreated hypothyroidism, but growth at about half the usual velocity for age is typical. It tends to be accompanied by delayed physical maturation so that bone maturation and puberty may be several years delayed. When severe GH deficiency is present from birth and never treated, adult heights can be as short as 48-65 inches (122–165 cm).

Severe GH deficiency in early childhood also results in slower muscular development, so that gross motor milestones such as standing, walking, and jumping may be delayed. Body composition (i.e., the relative amounts of bone, muscle, and fat) is affected in many children with severe deficiency, so that mild to moderate chubbiness is common (though GH deficiency alone rarely causes severe obesity). Some severely GH-deficient children have recognizable, cherubic facial features characterized by maxillary hypoplasia and forehead prominence (said to resemble a kewpie doll).

Other side effects in children include sparse hair growth and frontal recession, and pili torti and trichorrhexis nodosa are also sometimes present.

The principal feature of Laron syndrome is abnormally short stature (dwarfism). Physical symptoms include: prominent forehead, depressed nasal bridge, underdevelopment of mandible, truncal obesity, and micropenis in males. The breasts of females reach normal size, and in some are large in relation to body size. It has been suggested that hyperprolactinemia may contribute to the enlarged breast size. Seizures are frequently seen secondary to hypoglycemia. Some genetic variations decrease intellectual capacity. Laron syndrome patients also do not develop acne, except temporarily during treatment with IGF-1 (if performed).

In 2011, it was reported that people with this syndrome in the Ecuadorian villages are resistant to cancer and diabetes and are somewhat protected against aging. This is consistent with findings in mice with a defective growth hormone receptor gene.

Laron's syndrome, or Laron-type dwarfism, is an autosomal recessive disorder characterized by an insensitivity to growth hormone (GH), usually caused by a mutant growth hormone receptor. It causes short stature and an increased sensitivity to insulin which means that they are less likely to develop diabetes mellitus type 2 and possibly cancer as well. It can be treated with injections of recombinant IGF-1.

Growth hormone deficiency can be congenital or acquired in childhood or adult life. It can be partial or complete. It is usually permanent, but sometimes transient. It may be an isolated deficiency or occur in association with deficiencies of other pituitary hormones.

The term hypopituitarism is often used interchangeably with GH deficiency but more often denotes GH deficiency plus deficiency of at least one other anterior pituitary hormone. When GH deficiency (usually with other anterior pituitary deficiencies) is associated with posterior pituitary hormone deficiency (usually diabetes insipidus), the condition is termed panhypopituitarism.

The primary malformation apparent with JBS is hypoplasia (underdevelopment) of the nasal alae, or "wing of the nose". Both hypoplasia and aplasia (partial or complete absence) of structural cartilage and tissue in this area of the nose, along with the underlying alae nasi muscle, are prevailing features of the disorder. Together, these malformations give the nose and nostrils an odd shape and appearance.

Mental retardation ranging from mild to severe is present in the majority of JBS patients, and is related to the deleterious nature of the known mutagen responsible for the disorder and its effects on the developing central nervous system. Normal intelligence and age appropriate social development, however, have been reported in a few instances of JBS.

Symptoms include weakness, hypoglycemia, weight loss and decreased axillary and pubic hair. It can be either isolated or part of a generalised pituary dysfunction. It can be life-threatening if not recognised.

The symptoms of CAH vary depending upon the form of CAH and the sex of the patient. Symptoms can include:

Due to inadequate mineralocorticoids:

- vomiting due to salt-wasting leading to dehydration and death

Due to excess androgens:

- functional and average sized penis in cases involving extreme virilization (but no sperm)

- ambiguous genitalia, in some females, such that it can be initially difficult to identify external genitalia as "male" or "female".

- early pubic hair and rapid growth in childhood

- precocious puberty or failure of puberty to occur (sexual infantilism: absent or delayed puberty)

- excessive facial hair, virilization, and/or menstrual irregularity in adolescence

- infertility due to anovulation

- clitoromegaly, enlarged clitoris and shallow vagina

Due to insufficient androgens and estrogens:

- Undervirilization in XY males, which can result in apparently female external genitalia

- In females, hypogonadism can cause sexual infantilism or abnormal pubertal development, infertility, and other reproductive system abnormalities

It is usually diagnosed on basis of an ACTH or insulin tolerance test in combination with the clinical symptoms.

Congenital adrenal hyperplasia (CAH) are any of several autosomal recessive diseases resulting from mutations of genes for enzymes mediating the biochemical steps of production of mineralocorticoids, glucocorticoids or sex steroids from cholesterol by the adrenal glands (steroidogenesis).

Most of these conditions involve excessive or deficient production of sex steroids and can alter development of primary or secondary sex characteristics in some affected infants, children, or adults.

Sabinas brittle hair syndrome, also called Sabinas syndrome or brittle hair-mental deficit syndrome, is an autosomal recessive congenital disorder affecting the integumentary system.

Crandall syndrome is a very rare congenital disorder characterised by progressive sensorineural hearing loss, hair loss associated with pili torti, and hypogonadism demonstrated through low levels of luteinising hormone and growth hormone. It is thought to be an autosomal recessive disorder closely related to Björnstad syndrome which presents similarly but without hypogonadism.

The condition was first reported by B. F. Crandall in 1973.

Chronic illnesses, malnutrition, endocrine, metabolic disorders or chromosomal anomalies are characterized by proportionate short stature.

On the other hand, most genetic skeletal dysplasias are known for short stature that may be proportionate or disproportionate. Disproportionate short stature can be further subdivided as specified by the body segments affected by shortening, namely limbs versus trunk:

- Short-limb short stature in which there is limb shortening as achondroplasia, hypochondroplasia, pseudoachondroplasia and multiple epiphyseal dysplasia.

- Short-trunk short stature in which there is trunk shortening as spondyloepiphyseal dysplasia and mucopolysaccharidosis

Short-limb short stature can be further subcategorised in accordance with limb segment affected by shortening. These subcategories of limb shortening include, rhizomelic (humerus and femur), mesomelic (radius, ulna, tibia and fibula) and acromelic (hands and feet). Anthropometric measurements provide are very beneficial tools to the diagnostic process of genetic skeletal dysplasias. The anthropometric measurements include height, sitting height, arm span, upper/ lower-body segment ratio, sitting height/height ratio, and arm span/height ratio for age. They also aid in the differential diagnosis of skeletal dysplasia subtypes.

Congenital hypogonadotropic hypogonadism presents as hypogonadism, e.g., reduced or absent puberty, low libido, infertility, etc. due to an impaired release of the gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), and a resultant lack of sex steroid and peptides production by the gonads.

In Kallmann syndrome, a variable non-reproductive phenotype occurs with anosmia (loss of the sense of smell) including sensorineural deafness, coloboma, bimanual synkinesis, craniofacial abnormalities, and/or renal agenesis.

Kowarski syndrome describes cases of growth failure (height and bone age two standard deviations below the mean for age), despite the presence of normal or slightly high blood growth hormone by radioimmunoassay (RIA-GH) and low serum IGF1 (formerly called somatomedin), and who exhibit a significant increase in growth rate following recombinant GH therapy.

Symptoms include brittle hair, mild mental retardation and nail dysplasia. The syndrome was first observed in Sabinas, a small community in northern Mexico.

The principal biochemical features of the illness are reduced hair cystine levels, increased copper/zinc ratio, and presence of arginosuccinic acid in the blood and urine.

The key finding is brittle hair with low sulfur content, but alternating dark and light bands under polarizing microscopy, trichoschisis, and absent or defective cuticle are additional important clues for the diagnosis of trichothiodystrophy. Review of literature reveals extensive associated findings in trichothiodystrophy. Amino acid analyses of control hair when compared with those of patients with the Sabinas syndrome showed very striking differences with regard to content of sulphur amino acids. As in previous descriptions of amino acid abnormalities in the trichorrhexis nodosa of arginosuccinicaciduria, there were increases in lysine, aspartic acid, alanine, leucine, isoleucine, and tyrosine.

Trichothiodystrophy represents a central pathologic feature of a specific hair dysplasia associated with several disorders in organs derived from ectoderm and neuroectoderm. Trichothiodystrophy or TTD is a heterogeneous group of autosomal recessive disorders, characterized by abnormally sulfur deficient brittle hair and accompanied by ichthyosis and other manifestations.

Patients with trichothiodystrophy should have a thorough evaluation for other associated manifestations, including investigation of photosensitivity and DNA repair defects. Because the disease appears to be inherited in an autosomal recessive pattern, detection of low-sulfur brittle hair syndrome is also important for genetic counseling.

An inborn error of steroid metabolism is an inborn error of metabolism due to defects in steroid metabolism.

A variety of conditions of abnormal steroidogenesis exist due to genetic mutations in the steroidogenic enzymes involved in the process, of which include:

- 18,20-Desmolase (P450scc) deficiency: blocks production of all steroid hormones from cholesterol

- 3β-Hydroxysteroid dehydrogenase type 2 deficiency: impairs progestogen and androgen metabolism; prevents the synthesis of estrogens, glucocorticoids, and mineralocorticoids; causes androgen deficiency in males and androgen excess in females

- Combined 17α-hydroxylase/17,20-lyase deficiency: impairs progestogen metabolism; prevents androgen, estrogen, and glucocorticoid synthesis; causes mineralocorticoid excess

- Isolated 17,20-lyase deficiency: prevents androgen and estrogen synthesis

- 21-Hydroxylase deficiency: prevents glucocorticoid and mineralocorticoid synthesis; causes androgen excess in females

- 11β-Hydroxylase type 1 deficiency: impairs glucocorticoid and mineralocorticoid metabolism; causes glucocorticoid deficiency and mineralocorticoid excess as well as androgen excess in females

- 11β-Hydroxylase type 2 deficiency: impairs corticosteroid metabolism; results in excessive mineralocorticoid activity

- 18-Hydroxylase deficiency: impairs mineralocorticoid metabolism; results in mineralocorticoid deficiency

- 18-Hydroxylase overactivity: impairs mineralocorticoid metabolism; results in mineralocorticoid excess

- 17β-Hydroxysteroid dehydrogenase deficiency: impairs androgen and estrogen metabolism; results in androgen deficiency in males and androgen excess and estrogen deficiency in females

- 5α-Reductase type 2 deficiency: prevents the conversion of testosterone to dihydrotestosterone; causes androgen deficiency in males

- Aromatase deficiency: prevents estrogen synthesis; causes androgen excess in females

- Aromatase excess: causes excessive conversion of androgens to estrogens; results in estrogen excess in both sexes and androgen deficiency in males

In addition, several conditions of abnormal steroidogenesis due to genetic mutations in "receptors", as opposed to enzymes, also exist, including:

- Gonadotropin-releasing hormone (GnRH) insensitivity: prevents synthesis of sex steroids by the gonads in both sexes

- Follicle-stimulating (FSH) hormone insensitivity: prevents synthesis of sex steroids by the gonads in females; merely causes problems with fertility in males

- Luteinizing hormone (LH) insensitivity: prevents synthesis of sex steroids by the gonads in males; merely causes problems with fertility in females

- Luteinizing hormone (LH) oversensitivity: causes androgen excess in males, resulting in precocious puberty; females are asymptomatic

No activating mutations of the GnRH receptor in humans have been described in the medical literature, and only one of the FSH receptor has been described, which presented as asymptomatic.

Gonadotropin-releasing hormone (GnRH) insensitivity is a rare autosomal recessive genetic and endocrine syndrome which is characterized by inactivating mutations of the gonadotropin-releasing hormone receptor (GnRHR) and thus an insensitivity of the receptor to gonadotropin-releasing hormone (GnRH), resulting in a partial or complete loss of the ability of the gonads to synthesize the sex hormones. The condition manifests itself as isolated hypogonadotropic hypogonadism (IHH), presenting with symptoms such as delayed, reduced, or absent puberty, low or complete lack of libido, and infertility, and is the predominant cause of IHH when it does not present alongside anosmia.

Shortness in children and young adults nearly always results from below-average growth in childhood, while shortness in older adults usually results from loss of height due to kyphosis of the spine or collapsed vertebrae from osteoporosis.

From a medical perspective, severe shortness can be a variation of normal, resulting from the interplay of multiple familial genes. It can also be due to one or more of many abnormal conditions, such as chronic (prolonged) hormone deficiency, malnutrition, disease of a major organ system, mistreatment, treatment with certain drugs, chromosomal deletions. Human growth hormone (HGH) deficiency may occur at any time during infancy or childhood, with the most obvious sign being a noticeable slowing of growth. The deficiency may be genetic. Among children without growth hormone deficiency, short stature may be caused by Turner syndrome, chronic renal insufficiency, being small for gestational age at birth, Prader–Willi syndrome, Wiedemann-Steiner syndrome, or other conditions. Genetic skeletal dysplasias also known as osteochondrodysplasia usually manifest in short stature.

When the cause is unknown, it is called "idiopathic short stature".

Short stature can also be caused by the bone plates fusing at an earlier age than normal, therefore stunting growth. Normally, your bone age is the same as your biological age but for some people, it is older. For many people with advanced bone ages, they hit a growth spurt early on which propels them to average height but stop growing at an earlier age. However, in some cases, people who are naturally shorter combined with their advanced bone age, end up being even shorter than the height they normally would have been because of their stunted growth.

Estrogen insensitivity syndrome (EIS), or estrogen resistance, is a form of congenital estrogen deficiency or hypoestrogenism which is caused by a defective estrogen receptor (ER) – specifically, the estrogen receptor alpha (ERα) – that results in an inability of estrogen to mediate its biological effects in the body. Congenital estrogen deficiency can alternatively be caused by a defect in aromatase, the enzyme responsible for the biosynthesis of estrogens, a condition which is referred to as aromatase deficiency and is similar in symptomatology to EIS.

EIS is an extremely rare occurrence. As of 2016, there have been three published reports of EIS, involving a total of five individuals. The reports include a male case published in 1994, a female case published in 2013, and a familial case involving two sisters and a brother which was published in 2016.

EIS is analogous to androgen insensitivity syndrome (AIS), a condition in which the androgen receptor (AR) is defective and insensitive to androgens, such as testosterone and dihydrotestosterone (DHT). The functional opposite of EIS is hyperestrogenism, for instance that seen in aromatase excess syndrome.

Isolated hypogonadotropic hypogonadism (IHH), also called idiopathic or congenital hypogonadotropic hypogonadism (CHH), as well as isolated or congenital gonadotropin-releasing hormone deficiency (IGD), is a condition which results in a small subset of cases of hypogonadotropic hypogonadism (HH) due to deficiency in or insensitivity to gonadotropin-releasing hormone (GnRH) where the function and anatomy of the anterior pituitary is otherwise normal and secondary causes of HH are not present.

Lipoid congenital adrenal hyperplasia is an endocrine disorder that is an uncommon and potentially lethal form of congenital adrenal hyperplasia (CAH). It arises from defects in the earliest stages of steroid hormone synthesis: the transport of cholesterol into the mitochondria and the conversion of cholesterol to pregnenolone—the first step in the synthesis of all steroid hormones. Lipoid CAH causes mineralocorticoid deficiency in affected infants and children. Male infants are severely undervirilized causing their external genitalia to look feminine. The adrenals are large and filled with lipid globules derived from cholesterol.

Infants born with congenital hypothyroidism may show no effects, or may display mild effects that often go unrecognized as a problem: excessive sleeping, reduced interest in nursing, poor muscle tone, low or hoarse cry, infrequent bowel movements, exaggerated jaundice, and low body temperature. If fetal deficiency was severe because of complete absence (athyreosis) of the gland, physical features may include a larger anterior fontanel, persistence of a posterior fontanel, an umbilical hernia, and a large tongue (macroglossia).

In the era before newborn screening, less than half of cases of severe hypothyroidism were recognized in the first month of life. As the months proceeded, these babies would grow poorly and be delayed in their development. By several years of age, they would display the recognizable facial and body features of cretinism. Persistence of severe, untreated hypothyroidism resulted in severe mental impairment, with an IQ below 80 in the majority. Most of these children eventually ended up in institutional care.

Deficiency of all anterior pituitary hormones is more common than individual hormone deficiency.

Deficiency of luteinizing hormone (LH) and follicle-stimulating hormone (FSH), together referred to as the gonadotropins, leads to different symptoms in men and women. Women experience oligo- or amenorrhea (infrequent/light or absent menstrual periods respectively) and infertility. Men lose facial, scrotal and trunk hair, as well as suffering decreased muscle mass and anemia. Both sexes may experience a decrease in libido and loss of sexual function, and have an increased risk of osteoporosis (bone fragility). Lack of LH/FSH in children is associated with delayed puberty.

Growth hormone (GH) deficiency leads to a decrease in muscle mass, central obesity (increase in body fat around the waist) and impaired attention and memory. Children experience growth retardation and short stature.

Adrenocorticotropic hormone (ACTH) deficiency leads to adrenal insufficiency, a lack of production of glucocorticoids such as cortisol by the adrenal gland. If the problem is chronic, symptoms consist of fatigue, weight loss, failure to thrive (in children), delayed puberty (in adolescents), hypoglycemia (low blood sugar levels), anemia and hyponatremia (low sodium levels). If the onset is abrupt, collapse, shock and vomiting may occur. ACTH deficiency is highly similar to primary Addison's disease, which is cortisol deficiency as the result of direct damage to the adrenal glands; the latter form, however, often leads to hyperpigmentation of the skin, which does not occur in ACTH deficiency.

Thyroid-stimulating hormone (TSH) deficiency leads to hypothyroidism (lack of production of thyroxine (T4) and triiodothyronine (T3) in the thyroid). Typical symptoms are tiredness, intolerance to cold, constipation, weight gain, hair loss and slowed thinking, as well as a slowed heart rate and low blood pressure. In children, hypothyroidism leads to delayed growth and in extreme inborn forms to a syndrome called "cretinism".

Prolactin (PRL) plays a role in breastfeeding, and inability to breastfeed may point at abnormally low prolactin levels.

Chondrodystrophy (literally, "cartilage maldevelopment") refers to a skeletal disorder caused by one of myriad genetic mutations that can affect the development of cartilage. As a very general term it is only used in the medical literature when a more precise description of the condition is unavailable.