Based on the neurodevelopmental hypothesis of schizophrenia, neurotrophic factors (NTFs) may be involved in its pathogenesis. Previous association studies between schizophrenia and neurotrophic factors have shown inconsistent results, which might be due to the heterogeneity and small sample size of the studies. To reach a conclusive understanding of the association, we used a meta-analytic method to study the association of schizophrenia with the polymorphisms in two candidate genes, ciliary neurotrophic factor (CNTF) and neurotrophin 3 (NT3). In our study, two meta-analyses were performed. One included eight studies examining the association of schizophrenia with the A3 allele in a dinucleotide repeat polymorphism of the NT3 gene promoter (N=1938). The other was employed in nine studies examining the association with a null mutation of the CNTF gene (N=2393). Neither of these analyses provided evidence for association. However, our sub-analyses showed a trend of association between the NT3 polymorphism and schizophrenics in Japanese, as well as an association between the CNTF null mutation and schizophrenics without psychiatric family history. These results suggested that the variations at the NT3 and the CNTF genes do not influence the schizophrenia risk, but a role in the susceptibility of subgroups of the patients cannot be excluded.