Transgender people are a growing population with specific healthcare needs, barriers to care, and disease risk factors. Cultural competencies for working with transgender people in healthcare settings are essential to reduce barriers to care and combat the associated health disparities. Genetic counselors support their patients to understand and manage medically and personally complex life events and decisions. A genetic counselor caring for a transgender patient or a patient with a transgender relative will therefore require specific cultural competencies and medical knowledge that may not have been covered in their training. Transgender health is also a relatively young field in which new insights may quickly become fundamental. The present paper therefore provides an overview of current best practices for culturally sensitive working with transgender patients, and an introduction to the additional considerations for assessment of disease risk in transgender people. Guidance on how to ensure communication with patients and other stakeholders is inclusive and affirming of transgender identities, is offered. Medical interventions used for gender transitions are described, and their (potential) effects on cancer and cardiovascular disease risk are discussed. Furthermore, the effects of sociocultural risk factors such as minority stress are outlined. In sum, we invite the reader to consider the specific biological, psychological, and social context of the consultation. Finally, we explore culturally competent approaches to pedigree charting and physical examinations with transgender people and provide recommendations for practice.