The first challenge in diagnosing female sexual dysfunction(s) originates in our diagnostic system. The traditional model of classifying sexual dysfunction is anchored in the sexual response cycle: desire - arousal - orgasm - resolution. However, as some experts have pointed out, this classification may be problematic in the area of female sexuality. Both the diagnoses of female hypoactive sexual desire disorder (FHSDD) and female arousal disorder (FSAD) probably need to be redefined and refined. Examples include adding the lack of responsive desire to the FHSDD criteria and creating categories of subjective FSAD and genital FSAD.

The second challenge in diagnosis female dysfunction is the lack of solid diagnostic instruments, diagnosis-specific laboratory assays and other specific testing. Specific measures of female sexual functioning, such as Female Sexual Functioning Index, Profile of Female Sexual Functioning, Sexual Function Questionnaire, Sexual Desire and Interest Inventory, and Female Sexual Distress Scale were mostly developed as outcome measures. No solid diagnostic instrument for sexual dysfunction exists, not even a version of the Structured Clinical Interview for DSM sexual dysfunctions. The contribution of imaging techniques, such as ultrasonography, magnetic resonance imaging or thermography, to the diagnosis is unclear, and these techniques are far (if ever) from clinical use.

Thus, a detailed comprehensive clinical interview combined with physical examination, possibly a gynecological examination, and in some cases laboratory hormonal testing remains the cornerstone of diagnosing and assessing female sexual dysfunctions.