A nested variable number tandem repeats (VNTR) polymerase chain reaction (PCR) technique was developed for the direct typing of meningococcal PCR-positive clinical samples. The system was evaluated on a panel of 43 clinical samples and isolates positive for Neisseria meningitidis. The results revealed that VNTR-PCR can be used directly in clinical samples, allowing fine typing of N. meningitidis.