Low sexual desire alone is not equivalent to HSDD because of the requirement in HSDD that the low sexual desire causes marked distress and interpersonal difficulty and because of the requirement that the low desire is not better accounted for by another disorder in the DSM or by a general medical problem. It is therefore difficult to say exactly what causes HSDD. It is easier to describe, instead, some of the causes of low sexual desire.

In men, though there are theoretically more types of HSDD/low sexual desire, typically men are only diagnosed with one of three subtypes.

- Lifelong/generalised: The man has little or no desire for sexual stimulation (with a partner or alone) and never had.

- Acquired/generalised: The man previously had sexual interest in his present partner, but lacks interest in sexual activity, partnered or solitary.

- Acquired/situational: The man was previously sexually interested in his present partner but now lacks sexual interest in this partner but has desire for sexual stimulation (i.e. alone or with someone other than his present partner.)

Though it can sometimes be difficult to distinguish between these types, they do not necessarily have the same cause. The cause of lifelong/generalized HSDD is unknown. In the case of acquired/generalized low sexual desire, possible causes include various medical/health problems, psychiatric problems, low levels of testosterone or high levels of prolactin. One theory suggests that sexual desire is controlled by a balance between inhibitory and excitatory factors. This is thought to be expressed via neurotransmitters in selective brain areas. A decrease in sexual desire may therefore be due to an imbalance between neurotransmitters with excitatory activity like dopamine and norepinephrine and neurotransmitters with inhibitory activity, like serotonin. The, New York-based, "New View Campaign" organization has expressed skepticism about too much emphasis on explanations based on neurotransmitters because emphasis on such explanations have been made largely by "educational" efforts funded by Boehringer-Ingelheim while it was attempting to get the FDA to approve a drug affecting neurotransmitters for treatment for HSDD. Low sexual desire can also be a side effect of various medications. In the case of acquired/situational HSDD, possible causes include intimacy difficulty, relationship problems, sexual addiction, and chronic illness of the man’s partner. The evidence for these is somewhat in question. Some claimed causes of low sexual desire are based on empirical evidence. However, some are based merely on clinical observation. In many cases, the cause of HSDD is simply unknown.

There are some factors that are believed to be possible causes of HSDD in women. As with men, various medical problems, psychiatric problems (such as mood disorders), or increased amounts of prolactin can cause HSDD. Other hormones are believed to be involved as well. Additionally, factors such as relationship problems or stress are believed to be possible causes of reduced sexual desire in women. According to one recent study examining the affective responses and attentional capture of sexual stimuli in women with and without HSDD, women with HSDD do not appear to have a negative association to sexual stimuli, but rather a weaker positive association than women without HSDD

Hypoactive sexual desire disorder (HSDD) or inhibited sexual desire (ISD) is considered a sexual dysfunction and is characterized as a lack or absence of sexual fantasies and desire for sexual activity, as judged by a clinician. For this to be regarded as a disorder, it must cause marked distress or interpersonal difficulties and not be better accounted for by another mental disorder, a drug (legal or illegal), some other medical condition, or asexuality. A person with ISD will not start, or respond to their partner's desire for, sexual activity.

There are various subtypes. HSDD can be general (general lack of sexual desire) or situational (still has sexual desire, but lacks sexual desire for current partner), and it can be acquired (HSDD started after a period of normal sexual functioning) or lifelong (the person has always had no/low sexual desire.)

HSDD has garnered much criticism, primarily by asexual activists. They point out that HSDD puts asexuality in the same position homosexuality was from 1974-1987. The DSM at that time recognised 'ego-dystonic homosexuality' as a disorder, defined as sexual interest in the same sex that caused significant distress. The DSM itself officially recognized this as unnecessarily pathologizing homosexuality and removed it as a disorder in 1987.

The female sexual response system is complex and even today, not fully understood. The most prevalent of female sexual dysfunctions that have been linked to menopause include lack of desire and libido; these are predominantly associated with hormonal physiology. Specifically, it is the decline in serum estrogens that causes these changes in sexual functioning. Androgen depletion may also play a role, but currently this is less clear. The hormonal changes that take place during the menopausal transition have been suggested to affect women's sexual response through several mechanisms, some more conclusive than others.

Whether or not aging directly affects women's sexual functioning during menopause is another area of controversy. However, many studies, including Hayes and Dennerstein's critical review, have demonstrated that aging has a powerful impact on sexual function and dysfunction in women, specifically in the areas of desire, sexual interest, and frequency of orgasm. In addition, Dennerstien and colleagues found that the primary predictor of sexual response throughout menopause is prior sexual functioning. This means that it is important to understand how the physiological changes in men and women can affect their sexual desire. Despite the seemingly negative impact that menopause can have on sexuality and sexual functioning, sexual confidence and well-being can improve with age and menopausal status. Furthermore, the impact that a relationship status can have on quality of life is often underestimated.

Testosterone, along with its metabolite dihydrotestosterone, is extremely important to normal sexual functioning in men and women. Dihydrotestosterone is the most prevalent androgen in both men and women. Testosterone levels in women at age 60 are, on average, about half of what they were before the women were 40. Although this decline is gradual for most women, those who’ve undergone bilateral oophorectomy experience a sudden drop in testosterone levels; this is because the ovaries produce 40% of the body's circulating testosterone.

Sexual desire has been related to three separate components: drive, beliefs and values, and motivation. Particularly in postmenopausal women, drive fades and is no longer the initial step in a woman's sexual response (if it ever was).

The results of family and twin studies suggest that genetic factors play a role in the etiology of autism and other pervasive developmental disorders. Studies have consistently found that the prevalence of autism in siblings of autistic children is approximately 15 to 30 times greater than the rate in the general population. In addition, research suggests that there is a much higher concordance rate among monozygotic twins compared to dizygotic twins. It appears that there is no single gene that can account for autism. Instead, there seem to be multiple genes involved, each of which is a risk factor for components of the autism spectrum disorders.

Several prenatal and perinatal complications have been reported as possible risk factors for autism. These risk factors include maternal gestational diabetes, maternal and paternal age over 30, bleeding after first trimester, use of prescription medication (e.g. valproate) during pregnancy, and meconium in the amniotic fluid. While research is not conclusive on the relation of these factors to autism, each of these factors has been identified more frequently in autistic children compared to their non-autistic siblings and other normally developing youth.

Low vitamin D levels in early development has been hypothesized as a risk factor for autism.