Colostomy is a life-saving procedure in newborns with high anorectal malformations (ARM). However, the procedure may be attended by complications, particularly in resource limited settings. This is an evaluation of the morbidity and mortality following colostomy for ARM in newborns in two paediatric teaching centres in a developing country. A retrospective review of 61 neonates who had colostomy for high ARM in 4 years is conducted. The babies were categorised into Group A (weight at presentation < 2.5 kg) and Group B (weight at presentation > 2.5 kg). There were 47 boys and 14 girls aged 18 h to 28 days (median 6 days). There were 23 babies in Group A; 18 had colostomy under local anaesthetic (LA), 5 of whom died while 5 had the procedure done under general anaesthetic (GA), 3 of whom died (mortality 8/23, 34.78%). Group B consisted of 38 babies, 18 had colostomy under GA, 3 died, while in 20 the procedure was under LA, 1 of who died (mortality 4/38, 10.5%). The difference in mortality between groups A and B was statistically insignificant (p < 0.056). There were no significant differences in outcome between the two groups when the type of anaesthesia or types of colostomy were considered. Surgical site infection was the most common 12/61, 19.7%. Of the 12 babies that died, 7 were due to overwhelming infections, 4 respiratory insufficiencies and 1 cyanotic heart disease. The overall procedure related mortality was therefore 7 (11.5%). None of the centres had adequate neonatal intensive care services during the period of this report. Morbidity and mortality following colostomy for ARM in newborns is still high in this setting, due largely to infective complications, particularly in babies < 2.5 kg.