Low density lipoprotein is transcytosed across the blood-brain barrier mediated by low density lipoprotein receptor (LDLR). LDLR in the brain is mainly expressed on capillary endothelial cells and is therefore considered to be an important susceptibility gene in modifying the stroke presentation. A HapMap-based haplotype-tagging single nucleotide polymorphism association study was conducted in an isolated Taiwanese population. Two hundred and ninety-two unrelated patients with cerebral infarction, 76 patients with small vessel occlusion (SVO) disorder and 216 with non-SVO disorder were enrolled. For rs2738446, under the dominant model, the odds ratios (ORs) associated with the CC genotype were computed, with GG + CG carriers considered as the reference group. Homozygote CC carriers had a two-fold increased risk of SVO disorder [OR=2.0, 95% confidence interval (CI)=1.08-3.70, p=0.025). For rs2738450, under the dominant model, the ORs associated with the CC genotype were computed, with AA + AC carriers considered as the reference group. Homozygote CC carriers had a 1.85-fold increased risk of SVO disorder (OR=1.85, 95% CI=1.01-3.33, p=0.04). When analysing the association between the haplotype related to rs2738446 and rs2738450 and SVO disorder, the most common haplotype allele CC was used as the reference, and the GA haplotype allele was associated with a 48% decreased risk of SVO disorder (OR=0.52; 95% CI=0.29-0.93, p=0.029). Haplotype-based analysis of LDLR in Taiwanese patients with cerebral infarction provided preliminary evidence suggesting that genetic polymorphisms of LDLR can modify the stroke presentation.