<i>Background:</i> An association between versican <i>(CSPG2)</i>, perlecan <i>(HSPG2)</i>, fibrillin 2 <i>(FBN2)</i> and collagen 4A1 <i>(COL4A1)</i> gene variants and intracranial aneurysms (IA) has been reported in 2 studies analyzing Dutch IA patients. The aim of this study was to verify these associations in a Japanese IA population. In addition, a meta-analysis on the association of these genes and IA for the combined Dutch and Japanese populations was performed. <i>Methods:</i> The associated single nucleotide polymorphisms (SNPs) in these genes identified in the Dutch study were genotyped in 632 Japanese IA patients and 808 healthy control subjects using TaqMan SNP genotyping assays. <i>Results:</i> A similar association to that previously found in the Dutch population was found for the <i>CSPG2 </i>(rs251124) and <i>HSPG2</i> (rs3767137) SNPs, although both associations were not statistically significant in the Japanese population (<i>CSPG2 </i>OR 1.18, 95% CI 0.98–1.41, p = 0.08; <i>HSPG2</i> OR 1.09, 95% CI 0.90–1.32). Combining the Dutch and Japanese data for a meta-analysis showed an overall association between the <i>CSPG2 </i>SNP and IA (OR 1.29, 95% CI 1.12–1.48, p = 0.0005) and the <i>HSPG2</i> SNP and IA (OR 1.22, 95% CI 1.08–1.39, p = 0.002). No differences in SNP frequency were observed for <i>FBN2</i> and <i>COL4A1</i> between Japanese patients and controls. <i>Conclusions:</i> By analyzing <i>HSPG2</i>, <i>CSPG2</i>, <i>FBN2</i> and <i>COL4A1</i>, we were able to replicate the association of <i>CSPG2 </i>and show that there is a trend for HSPG2 towards association in the Japanese IA population by means of a meta-analysis combining the Dutch and Japanese results. The association of <i>FBN2</i> and <i>COL4A1 </i>could not be replicated in the Japanese IA population.