This case report describes the diagnostic approach to an 18-year-old woman, known with Asperger's syndrome (AS). She presented with abdominal pain, weight loss, nausea and a loss of appetite. Ultrasound and magnetic resonance imaging showed polycystic kidney disease (PKD) and agenesis of the dorsal pancreas (DPA). Genetic testing revealed a 1.5 mega-base deletion at chromosome 17q12, which included the HNF1β. She was diagnosed with 17q12 microdeletion syndrome, which could explain the presence of both DPA, PKD and AS.