Major depression (MD) is a common psychiatric disorder and one of its most serious symptoms is suicidal ideation. Six polymorphisms in four genes related to the serotonin system, including the HTTLPR and HTTVNTR in the SLC6A4 gene, rs6295 in the HTR1A gene, rs11568817 and rs130058 in the HTR1B gene, and rs6313 in the HTR2A gene, were studied in 420 patients with MD to investigate the relationship between these genes and suicidal ideation in MD. An allele association study revealed a significant relationship between rs11568817 and suicidal ideation, while no association was found for any of the other five polymorphisms. A haplotype association study suggested that the rs11568817-rs130058 haplotype of the HTR1B gene is significantly associated with suicidal ideation in MD. No association was found between suicidal ideation and the combined effect of the genes studied using rs11568817 as a conditional marker. Our work indicated that the HTR1B gene might be involved in the development of suicidal ideation in MD among a Chinese Han population.