HYPOTHALAMIC AMENORRHOEA AS AN EXTRAINTESTINAL MANIFESTATION OF CROHN’S DISEASE: A CASE REPORT Crohn’s disease (CD), a chronic inflammatory bowel condition, although rare in Malaysia, can present with atypical systemic features, including reproductive dysfunction. We report the case of a 31-year-old woman referred for secondary amenorrhoea and presumed endometriosis, later diagnosed with CD following worsening gastrointestinal symptoms and significant weight loss. Hormonal evaluation revealed hypothalamic–pituitary axis suppression secondary to malnutrition and systemic inflammation. Treatment with corticosteroids and nutritional rehabilitation led to weight gain and resumption of menses within 3 months. This case highlights the importance of recognising functional hypothalamic amenorrhoea as a reversible consequence of chronic illness and nutritional deficiency. It also underscores how systemic diseases such as CD may mimic gynaecological conditions, potentially delaying accurate diagnosis. Early multidisciplinary collaboration is essential in evaluating menstrual disturbances with overlapping gastrointestinal symptoms, especially in regions where inflammatory bowel disease remains uncommon.