Nogo is a myelin-associated protein associated with neurite outgrowth and regeneration. A previous study has reported an association between an insertion/deletion polymorphism in schizophrenia. We tested for the distribution of the polymorphism and haplotypes of this and another insertion/deletion polymorphism in our population. We have also developed an assay combining allele-specific polymerase chain reaction (AS-PCR) and restriction fragment length polymorphism (RFLP) to simultaneously type these two insertion/deletion polymorphisms. There was a statistically significant difference at the allelic level for both the CAA (chi2 = 4.378, df = 1, P value = 0.036) and TATC (chi2 = 5.807, df = 1, P = 0.016) polymorphisms in the female subgroup, but not in males. With our genotyping method, we also determined the molecular haplotype. Within the female gender, odds ratio is at 1.57 (95% CI 1.05-2.37) for CAACAA-TATC and 1.40 (95% CI 0.55-3.60) for CAA-TATC, the two at-risk haplotypes. Odds ratio is 0.63 (95% CI 0.42-0.93) for the protective wildtype haplotype CAA-TATCTATC. Further study of these two polymorphisms to investigate functional significance and confirm gender-specific association should be carried out.