Transgender people experience distress due to gender incongruence (i.e., a discrepancy between their gender identity and sex assigned at birth). Gender-affirming hormone treatment (GAHT) is a part of gender reassignment treatment. The therapeutic goals of the treatment are to develop the physical characteristics of the affirmed gender as far as possible. Guidelines have been developed for GAHT, which recommend dosage as well as different formulations of oestrogen and testosterone for treatment. Questions arise about the metabolic side effects of hormone treatment. Establishing reference ranges for common analytes in transgender individuals remains a task for laboratory medicine. It has been suggested once GAHT is commenced, the reference ranges for affirmed gender are reported for red blood cells, haemoglobin and haematocrit. For transgender assigned-female-at-birth (AFAB) people, testosterone concentrations are recommended to be within the reference interval established for cisgender men and for transgender assigned-male-at-birth (AMAB) people, estradiol concentrations are within the reference range for cisgender women. Sex-specific reference ranges are available for certain laboratory tests, and these may be organ (e.g., heart)-specific. Transgender-specific reference ranges may be a requirement for such tests. Laboratories may need to make decisions on how to report other tests in the transgender population, e.g., eGFR. Interpretation of further tests (e.g., reproductive hormones) can be individualized depending on clinical information. Electronic medical record systems require fields for gender identity/biological sex at birth so that laboratory results can be flagged appropriately. In this review, we aim to summarise the current position of the role of the laboratory in the clinical care of the transgender individual. Prior to the review, we will summarise the genetics of sex determination, the aetiology of gender incongruence, and the recommendations for GAHT and monitoring for the transgender population.