In 1990, Lukwiya earned a scholarship to earn a master's degree in tropical paediatrics in Liverpool School of Tropical Medicine. Despite being offered a teaching position at the school, where he earned the best marks in the school's history, he appears to have never considered any other option than returning to St. Mary's. Under Lukwiya's administration the hospital tripled its capacity to 18,000 patients annually, included wounded from both sides of the conflict, and a further 500 out-patients daily. St. Mary's became easily the best hospital in northern Uganda, arguably the best in the country and one of the top hospitals in East Africa. In December 1998, Lukwiya moved his family to the capital city, Kampala, far from the violence of the northern war. There he sought a master's in public health at Makerere University, leaving the running of the hospital to colleague Cyprian Opira. In 1999, Lukwiya, always a church-going Protestant, took his born-again wife to a Pentecostal church and declared that he too was born again.