This study was conducted during the 2004-2006 epidemic of meningitis in Sudan to follow-up the frequency of disease outbreak or endemic waves and to evaluate the new quadrivalent vaccine for actual application. Samples were collected from Darfur, El Gedaref, Kassala and Khartoum States and transported to the National Health Central Laboratory in Khartoum. Of 196 patients with clinical symptoms and signs of meningitis, conventional culture identified Neisseria meningitidis in 37 (189%), confirmed by polymerase chain reaction. N. meningitidis type A was identified in 29 (78.4%) patients, type C in 3 (8.1%) and N. meningitidis W135 in 5 (15.5%). The serotyping and molecular diagnosis patterns of N. meningitidis showed the emergence of the new strain, W135, in 5 (15.5%). The patients from the borders of Sudan, 3 from the West Darfur, and 1 each from El Gedaref and Kassala. These could be related to the movement of pilgrims through the borders to Saudi Arabia in the Hajj season. Serious consideration may be needed for quadrivalent vaccination to prevent seasonal and Hajj season outbreaks.