Chowdhury was transferred to Baghdad, Iraq as deputy country director in mid-2001. Prior to U.S. led invasion Chowdhury, along with his team was evacuated to larnaca, cyprus and was entrusted to prepare "Iraq reconstruction plan." In May 2003. he returned to Baghdad and continued till July. The United Nations Office in Baghdad was destroyed in August and 23 UN officials including the special representative of the secretary general were killed.