We present a case of non-functioning kidney secondary to a parapelvic cyst in a 45-year-old male who was investigated for a single episode of self-limiting left-sided flank pain. Initial contrast-enhanced computerized tomography (CT) with delayed phases showed a 4 cm left parapelvic cyst and mild renal pelvis dilatation with no other features of obstruction. A Mercaptoacetyltriglycine (MAG3) functional scan showed 52% split function in the affected kidney and prompt drainage with no evidence of obstruction. Although completely asymptomatic after the initial episode we opted to follow him up. Eighteen months on we discovered an atrophic kidney on repeat imaging with a split function of 9% with no change in parapelvic cyst size. We propose that an intermittent silent obstruction, caused by infundibular compression deep inside the kidney, may have caused calyceal dilatation and eventual loss of function in this case. We discuss this rare presentation, review the literature and propose a follow up plan. Level of evidence: Level 5