We report our experience of staged operations in the surgical treatment of complex jejuno-ileal atresia. Our study examined transgastric deflation of the proximal segment and feeding jejunostomy through the distal segment as a first stage followed by a definitive restoration of continuity secondarily at a tertiary centre over a period of three years. A cohort of 21 cases were studied. None suffered with intestinal perforation or volvulus. Tube plugging was seen in three patients who were relieved by flushing. Tube replacement was not required. One patient developed necrotising enterocolitis and died. Sepsis was seen in three. The age at the second operation was 56.2 ± 6.6 days. There was no complication after this second procedure. We therefore recommend this staged management for complex jejuno-ileal atresia, but suggest further studies.