The class 1 outer membrane protein encoded by the porA gene of Neisseria meningitidis is a candidate for a vaccine against meningococcal infection. The expression of class 1 outer membrane protein displays phase variation between three expression levels. Northern (RNA) blot and primer extension analysis revealed that this phase variation is regulated at the transcriptional level. The start site for transcription is located 59 bp upstream of the translational initiation codon. Sequence analysis of the promoter region of the porA gene of a variant without class 1 protein expression revealed nine contiguous guanidine residues between the -10 and -35 domains. Comparison of promoter sequences of different phase variants indicated that the length of the polyguanidine stretch correlated with the expression level of the class 1 outer membrane protein; the presence of 11, 10, or 9 contiguous guanidine residues results in high levels, medium levels, or no expression of class 1 mRNA, respectively. These results suggest that the variable porA expression levels seen in different isolates are modulated by guanidine residue insertion and/or deletion due to slipped-strand mispairing on the polyguanidine stretch within the intervening sequence of the -35 and -10 regions of the promoter. The phase variation of class 1 outer membrane protein may provide a molecular mechanism to evade the host immune defense. Therefore, the protective efficacy of a vaccine based on class 1 outer membrane protein may be questioned.