The risk of germ cell cancer (GCC) is elevated in many disorders of sex development (DSD) patients, although not to the same extent. A number of risk factors have been identified recently, but their interplay and relative impact is currently not fully clear. This paper offers guidance on how theoretical knowledge on GCC risk can be translated to the clinical setting, taking into account individual patient characteristics. Guidelines for decision making in different patient groups, based on a literature review, epidemiological evidence, pathological and clinical research, and personal experience are offered. Until the advent of reliable screening tools for the detection of pre-invasive cancer lesions, managing germ cell tumour risk focuses on the question of if and when to perform biopsy or gonadectomy in most patients, and how to interpret the histological findings.