Between 2005 and 2006, clinical specimens were collected from 31 infants with suspected congenital rubella syndrome (CRS) who presented at six hospitals in Khartoum, Sudan. Eleven (35.5%) were laboratory confirmed as CRS cases by testing for anti-rubella IgM, IgG and viral genome. For the first time in Sudan, the rubella virus genome was directly detected in clinical specimens of six CRS cases and two viruses were isolated in cell culture. Phylogenetic analysis suggested that three genotypes of rubella virus (RV; 1E, 2B and 1G) were co-circulating in Sudan. The study introduced the methodology for CRS confirmation and surveillance in Sudan and provides preliminary data.