A 50-year-old developmentally delayed male with Down's syndrome presented with recurrent episodes of hydronephrosis caused by an ectopic left thoracic kidney inside a Bochdalek hernia. This kidney had become hypofunctioning and eventually mandated surgical resection for chronic infection. Although Down's syndrome is more typically associated with Morgagni hernia, the multifactorial genetical etiology of congenital diaphragmatic hernias is further reinforced by the rather rare finding of an ectopic thoracic kidney herniating through the foramen of Bochdalek. Portions of his transverse colon, stomach and spleen were also displaced. The patient underwent laparoscopic diaphragmatic hernia repair and what we believe to be the first reported case of a trans-diaphragmatic nephrectomy of a non-functioning thoracic kidney. A laparoscopic approach was used to reduce the contents of the hernia, including stomach, spleen, transverse colon, and splenic flexure. The dysfunctional kidney was then resected via the hernia defect off its aberrant thoracic anatomy in situ. The hernia defect was repaired primarily and buttressed with a synthetic mesh. The patient was discharged uneventfully on post-op day 3. A follow-up CT scan one year later demonstrated the hernia repair to be intact. Our surgical technique and problem-solving for this unique case are demonstrated.