Links between maternal smoking and TDS are tenuous, but there are stronger associations between maternal alcohol consumption and incidences of cryptorchidism in sons. Smoking does however affect the growth of a fetus, and low birth weight is shown to increase the likelihood of all the disorders encompassed by TDS. Maternal obesity, resulting in gestational diabetes, has also been shown to be a risk factor for impaired testes development and TDS symptoms in sons.

Central to the cause of irreversible TDS are disruptions to early fetal testes development. This has both genetic, environmental, and lifestyle components, however the rapid increase in the incidence of the disorders associated with TDS in the last decades indicates that it is under a powerful environmental influence. The fetal origins of TDS are reinforced by the high incidence of TDS disorders found occurring together in one individual.

Approximately 1 in 20,000 individuals with a male appearance have 46,XX testicular disorder.

Microdeletions in the Y chromosome have been found at a much higher rate in infertile men than in fertile controls and the correlation found may still go up as improved genetic testing techniques for the Y chromosome are developed.

Much study has been focused upon the "azoospermia factor locus" (AZF), at Yq11. A specific partial deletion of AZFc called "gr/gr deletion" is significantly associated with male infertility among Caucasians in Europe and the Western Pacific region.

Additional genes associated with spermatogenesis in men and reduced fertility upon Y chromosome deletions include RBM, DAZ, SPGY, and TSPY.

Individuals with CAVD can reproduce with the assistance of modern technology with a combination of testicular sperm extraction and intracytoplasmic sperm injection (ICSI). However, as the risk of either cystic fibrosis or renal agenesis is likely to be higher in the children, genetic counseling is generally recommended.

The observation has been made many times that globozoospermia arises in siblings which points towards an underlying genetic cause. Recent progress has been made into determining what genes could be implicated in this pathology, with the previously mentioned genes being found to play a role. There are more genes which have been shown to be mutated in globozoospermia in mice, but these are yet to be connected to the human disease process. Examples of these include Gopc, Hrb and Csnka2. There are thousands of genes which guide the process of spermatogenesis, and knowing how they’re involved in globozoospermia is an important current area of research.

At puberty, most affected individuals require treatment with the male sex hormone testosterone to induce development of male secondary sex characteristics such as facial hair and deepening of the voice (masculinization). Hormone treatment can also help prevent breast enlargement (gynecomastia). Adults with this disorder are usually shorter than average for males and are unable to have children (infertile).

There is increasing evidence that the harmful products of tobacco smoking may damage the testicles and kill sperm, but their effect on male fertility is not clear. Some governments require manufacturers to put warnings on packets. Smoking tobacco increases intake of cadmium, because the tobacco plant absorbs the metal. Cadmium, being chemically similar to zinc, may replace zinc in the DNA polymerase, which plays a critical role in sperm production. Zinc replaced by cadmium in DNA polymerase can be particularly damaging to the testes.

Pre-testicular factors refer to conditions that impede adequate support of the testes and include situations of poor hormonal support and poor general health including:

- Hypogonadotropic hypogonadism due to various causes

- Obesity increases the risk of hypogonadotropic hypogonadism. Animal models indicate that obesity causes leptin insensitivity in the hypothalamus, leading to decreased Kiss1 expression, which, in turn, alters the release of gonadotropin-releasing hormone (GnRH).

- Undiagnosed and untreated coeliac disease (CD). Coeliac men may have reversible infertility. Nevertheless, CD can present with several non-gastrointestinal symptoms that can involve nearly any organ system, even in the absence of gastrointestinal symptoms. Thus, the diagnosis may be missed, leading to a risk of long-term complications. In men, CD can reduce semen quality and cause immature secondary sex characteristics, hypogonadism and hyperprolactinaemia, which causes impotence and loss of libido. The giving of gluten free diet and correction of deficient dietary elements can lead to a return of fertility. It is likely that an effective evaluation for infertility would best include assessment for underlying celiac disease, both in men and women.

- Drugs, alcohol

- Strenuous riding (bicycle riding, horseback riding)

- Medications, including those that affect spermatogenesis such as chemotherapy, anabolic steroids, cimetidine, spironolactone; those that decrease FSH levels such as phenytoin; those that decrease sperm motility such as sulfasalazine and nitrofurantoin

- Genetic abnormalities such as a Robertsonian translocation

In about 30% of infertile men no causative factor is found for their decrease in sperm concentration or quality by common clinical, instrumental, or laboratory means, and the condition is termed "idiopathic" (unexplained). A number of factors may be involved in the genesis of this condition, including age, infectious agents ( such as "Chlamydia trachomatis"), Y chromosome microdeletions, mitochondrial changes, environmental pollutants, and "subtle" hormonal changes.

A review in 2013 came to the result that oligospermia and azoospermia are significantly associated with being overweight (odds ratio 1.1), obese (odds ratio 1.3) and morbidly obese (odds ratio 2.0), but the cause of this is unknown. It found no significant relation between oligospermia and being underweight.

Testicular factors refer to conditions where the testes produces semen of poor quality despite adequate hormonal support and include:

- Age

- Genetic defects on the Y chromosome

- Y chromosome microdeletions

- Abnormal set of chromosomes

- Klinefelter syndrome

- Neoplasm, e.g. seminoma

- Cryptorchidism

- Varicocele (14% in one study)

- Trauma

- Hydrocele

- Mumps

- Malaria

- Defects in USP26 enzyme in some cases

Mast cells releasing inflammatory mediators appear to directly suppress sperm motility in a potentially reversible manner, and may be a common pathophysiological mechanism for several of the above-mentioned factors.

Idiopathic azoospermia is where there is no known cause of the condition. It may be a result of multiple risk factors, such as age and weight. For example, a review in 2013 came to the result that oligospermia and azoospermia are significantly associated with being overweight (odds ratio 1.1), obese (odds ratio 1.3) and morbidly obese (odds ratio 2.0), but the cause of this is unknown. The review found no significant relation between oligospermia and being underweight.

There are two main populations of CAVD; the larger group is associated with

cystic fibrosis and occurs because of a mutation in the CFTR gene, while the smaller group (estimated between 10 and 40%) is associated with Unilateral Renal agenesis (URA). The genetic basis of this second group is not well understood.

Mutation of the CFTR gene is found to result in obstructive azoospermia in postpubertal males with cystic fibrosis. Strikingly, CAVD is one of the most consistent features of cystic fibrosis as it affects 98-99% of individuals in this CF patient population. In contrast, acute or persistent respiratory symptoms present in only 51% of total CF patients.

In the subset of males with both CBAVD and URA, the CFTR mutation has been shown to occur at a rate only slightly higher than the overall population. Thus, McCallum, et al. have suggested another mutation may be responsible for this condition.

As the syndrome is due to a chromosomal non-disjunction event, the recurrence risk is not high compared to the general population. There has been no evidence found that indicates non-disjunction occurs more often in a particular family.

Globozoospermia (also known as round-headed sperm syndrome) is a rare and severe form of monomorphic teratozoospermia. This means that the spermatozoa show the same abnormality, and over 85% of spermatozoa in sperm have this abnormality. Globozoospermia is responsible for less than 0.1% of male infertility. It characterised by round-headed spermatozoa without acrosome, an abnormal nuclear membrane and midpiece defects. Affected males therefore suffer from either reduced fertility or infertility. Studies suggest that globozoospermia can be either total (100% round-headed spermatozoa without acrosomes) or partial (20-60% round acrosomeless spermatozoa with normal sperm also identified in the sperm count,) however it is unclear whether these two forms are variations on the same syndrome, or actually different syndromes.

Studies have suggested mutations or deletions in three genes are responsible for this condition: SPATA16, PICK1 and DPY19L2. ICSI (intracytoplasmic sperm injection) has previously been used to assist reproduction in globozoospermic patients, however it has not been particularly effective in all patients, due to low fertilisation rates.

Genetic factors can cause pretesticular, testicular, and posttesticular azoospermia (or oligospermia) and include the following situations: The frequency of chromosomal abnormalities is inversely proportional to the semen count, thus males with azoospermia are at risk to have a 10–15% (other sources citing 15–20% incidence) abnormalities on karyotyping versus about <1 % in the fertile male population.

Pretesticular azoospermia may be caused by congential hypopituitarism, Kallmann syndrome, Prader-Willi syndrome and other genetic conditions that lead to GnRH or gonadotropin deficiency.

Testicular azoospermia is seen in Klinefelter syndrome(XXY) and the XX male syndrome. In addition, 13% of men with azoospermia have a defective spermatogenesis that is linked to defects of the Y chromosome. Such defects tend to be de novo micro-deletions and affect usually the long arm of the chromosome. A section of the long arm of the Y chromosome has been termed Azoospermia Factor (AZF) at Yq11 and subdivided into AZFa, AZFb, AZFc and possibly more subsections. Defects in this area can lead to oligospermia or azoospermia, however, a tight genotype-phenotype correlation has not been achieved.

Spermatogenesis is defective with gene defects for the androgen receptor.

Posttesticular azoospermia can be seen with certain point mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene commonly associated with congenital vas deferens abnormalities.

Genetic counselling is indicated for men with genetic causes of azoospermia. In terms of reproduction, it needs to be considered if the genetic defect could be transmitted to the offspring.

The mechanism of mutation is not different for Y-chromosome microdeletion. However, the ability to repair it differs from other chromosomes. The human Y chromosome is passed directly from father to son, and is not protected against accumulating copying errors, whereas other chromosomes are error corrected by recombining genetic information from mother and father. This may leave natural selection as the primary repair mechanism for the Y chromosome.

A 1998 review noted that life expectancy is usually normal, but that there have occasionally been reported neonatal deaths due to PCD. A 2016 longitudinal study followed 151 adults with PCD for a median of 7 years. Within that span, 7 persons died with a median age of 65.

The causes of teratozoospermia are unknown in most cases. However, Hodgkin's disease, coeliac disease, and Crohn's disease may contribute in some instances. Lifestyle and habits (smoking, toxin exposure, etc.) can also cause poor morphology. Varicocele is another condition that is often associated with decreased normal forms (morphology).

In cases of globozoospermia (sperm with round heads), the Golgi apparatus is not transformed into the acrosome that is needed for fertilization.

The presence of abnormally-shaped sperm can negatively affect fertility by preventing transport through the cervix and/or preventing sperm from adhering to the ovum. Achieving a pregnancy may be difficult.

In testing for teratozoospermia, sperm are collected, stained and analyzed under a microscope to detect abnormalities. These abnormalities may include heads that are large, small, tapered, or pyriform or tails that are abnormally shaped.

Antiestrogens have been shown to be effective in the treatment of teratozoospermia.

Teratozoospermia (including the "globozoospermia" type), may be treated by intracytoplasmic sperm injection (ICSI), injecting sperm directly into the egg. Once the egg is fertilized, abnormal sperm morphology does not appear to influence blastocyst development or blastocyst morphology. Even with severe teratozoospermia, microscopy can still detect the few sperm cells that have a "normal" morphology, allowing for optimal success rate.

The cause of 48, XXXY can be from non-disjunction in the paternal sperm or non-disjunction in the maternal oocyte. The most likely scenario for the existence of this aneuploidy is that each parent (maternal and paternal) equally contributed to it, by the mother giving an XX and the father giving an XY.

In the case where the sperm is the genetic cause of 48, XXXY syndrome, the sperm would have to contain two X chromosomes and one Y chromosome. This would be caused by two non-disjunction events in spermatogenesis, both meosis I and meosis II. The duplicated X chromosome in the sperm would have to fail to separate in both meosis I and meosis II for a sperm as well as the X and Y chromosomes would have to be in the same sperm. Then the XXY sperm would fertilize a normal oocyte to make a XXXY zygote.

In the case where the oocyte is the genetic cause of 48, XXXY syndrome the oocyte would contain three X chromosome. This would be caused by two non-disjunction events during oogenesis. In meosis I both sets of duplicated X chromosomes would have to be not separated. Then in meosis II one set of X chromosomes would have to not separate and the other set would separate resulting in one oocyte with three X chromosomes. A normal sperm containing a Y chromosome would have to fertilize the XXX oocyte to make a XXXY zygote.

According to the American Society for Reproductive Medicine (ASRM), Age, Smoking, Sexually Transmitted Infections, and Being Overweight or Underweight can all affect fertility.

In broad sense, acquired factors practically include any factor that is not based on a genetic mutation, including any intrauterine exposure to toxins during fetal development, which may present as infertility many years later as an adult.

Factors that can cause male as well as female infertility are:

- DNA damage

- DNA damage reduces fertility in female ovocytes, as caused by smoking, other xenobiotic DNA damaging agents (such as radiation or chemotherapy) or accumulation of the oxidative DNA damage 8-hydroxy-deoxyguanosine

- DNA damage reduces fertility in male sperm, as caused by oxidative DNA damage, smoking, other xenobiotic DNA damaging agents (such as drugs or chemotherapy) or other DNA damaging agents including reactive oxygen species, fever or high testicular temperature

- General factors

- Diabetes mellitus, thyroid disorders, undiagnosed and untreated coeliac disease, adrenal disease

- Hypothalamic-pituitary factors

- Hyperprolactinemia

- Hypopituitarism

- The presence of anti-thyroid antibodies is associated with an increased risk of unexplained subfertility with an odds ratio of 1.5 and 95% confidence interval of 1.1–2.0.

- Environmental factors

- Toxins such as glues, volatile organic solvents or silicones, physical agents, chemical dusts, and pesticides. Tobacco smokers are 60% more likely to be infertile than non-smokers.

German scientists have reported that a virus called Adeno-associated virus might have a role in male infertility, though it is otherwise not harmful. Other diseases such as chlamydia, and gonorrhea can also cause infertility, due to internal scarring (fallopian tube obstruction).

Twelve percent of all infertility cases are a result of a woman either being underweight or overweight. Fat cells produce estrogen, in addition to the primary sex organs. Too much body fat causes production of too much estrogen and the body begins to react as if it is on birth control, limiting the odds of getting pregnant. Too little body fat causes insufficient production of estrogen and disruption of the menstrual cycle. Both under and overweight women have irregular cycles in which ovulation does not occur or is inadequate. Proper nutrition in early life is also a major factor for later fertility.

A study in the US indicated that approximately 20% of infertile women had a past or current eating disorder, which is five times higher than the general lifetime prevalence rate.

A review from 2010 concluded that overweight and obese subfertile women have a reduced probability of successful fertility treatment and their pregnancies are associated with more complications and higher costs. In hypothetical groups of 1000 women undergoing fertility care, the study counted approximately 800 live births for normal weight and 690 live births for overweight and obese anovulatory women. For ovulatory women, the study counted approximately 700 live births for normal weight, 550 live births for overweight and 530 live births for obese women. The increase in cost per live birth in anovulatory overweight and obese women were, respectively, 54 and 100% higher than their normal weight counterparts, for ovulatory women they were 44 and 70% higher, respectively.

Sertoli cell only syndrome is like other non-obstructive azoospermia (NOA) cases are managed by sperm retrieval through testicular sperm extraction (mTESE), micro-surgical testicular sperm extraction (mTESE), or testicular biopsy. On retrieval of viable sperm this could be used in Intracytoplasmic Sperm injection ICSI

In 1979, Levin described germinal cell aplasia with focal spermatogenesis where a variable percentage of seminiferous tubules contain germ cells. It is important to discriminate between both in view of ICSI.

A retrospective analysis performed in 2015 detailed the outcomes of N=148 men with non-obstructive azoospermia and diagnosed Sertoli cell-only syndrome:

- Men with SCOS: 148

- Testicular sperm was successfully retrieved: 35/148

- Successful ICSI: 20/148

- Clinical pregnancy: 4/148

This study considers the effect of FSH levels on clinical success, and it excludes abnormal karyotypes. All patients underwent MD-TESE in Iran. Ethnicity and genetic lineage may have an impact on treatment of azoospermia [citation needed].