Functional urological and gastrointestinal disorders are interrelated and characterized by a chronic course and considerable treatment resistance. Urological disorders associated with a sizeable functional effect include overactive bladder (OAB), interstitial cystitis/bladder pain syndrome (IC/BPS), and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). Poor treatment outcomes might be attributable to untreated underlying psychological and psychiatric disorders, as the co-occurrence of functional urological and gastrointestinal disorders with mood and anxiety disorders is common. The hypothetical bladder-gut-brain axis (BGBA) is a useful framework under which this interaction can be studied, suggesting that functional disorders represent a sensitized response to earlier threats such as childhood adversity or previous traumatic events, resulting in perceived emotional and bodily distress - the symptoms of functional disorders. Psychological and physical stress pathways might contribute to such alarm falsification, and neuroticism could be a risk factor for the co-occurrence of functional disorders and affective conditions. Additionally, physical threat - either from external sources or internal sources such as infection - might contribute to alarm falsification by influencing body-brain crosstalk on homeostasis and, therefore, affecting mood, cognition, and behaviour. Multidisciplinary research and an integrated care approach is, therefore, required to further elucidate and remediate functional urological and gastrointestinal polymorphic phenotypes.