Background: Genetic testing is an increasingly important component in the diagnostic evaluation of kidney diseases. Pathogenic variants in the HNF1B gene cause a disorder classically known as renal cysts and diabetes (RCAD) syndrome, typically characterised by bilateral renal cysts, diabetes mellitus, and a broad spectrum of other extrarenal abnormalities. However, non-cystic presentations often lead to diagnostic delays. Case Report: We report the case of a 28-year-old woman evaluated for chronic kidney disease of unknown aetiology who presented with atypical radiological findings. Imaging revealed bilateral renal hypoplasia completely devoid of cystic transformation. The patient exhibited no proteinuria, electrolyte or acid–base disturbances, diabetes mellitus, or pancreatic abnormalities. Next-generation sequencing identified pathogenic HNF1B missense variant (p.Met160Val), confirming the diagnosis of genetic kidney disease. The patient’s clinical course remained stable throughout the follow-up period. Conclusions: This case illustrates the marked phenotypic heterogeneity of HNF1B-associated disease and supports incorporating genetic testing in patients with unexplained structural kidney abnormalities, even in the absence of classical cystic renal disease or typical extrarenal manifestations, to ensure accurate diagnosis and treatment, and to facilitate appropriate family counselling.