Interest in genome-wide association studies to identify susceptibility alleles for cancer is growing, and several are currently planned or under way. Although the feasibility of collecting buccal cell samples as an alternative to venous blood samples as a source of genomic DNA has been shown, the validity of using DNA from buccal cells for genome-wide scans has not been assessed. We used 46 paired buffy coat and buccal cell samples to test the feasibility of using DNA from buccal cells for genotyping with the HumanHap300 Bead Chip (v.1.0.0) on the Illumina Infinium II platform. Genotyping was successful in every sample, regardless of DNA yield or sample type. Of the 317,502 genotypes attempted, 315,314 (99.3%) were successfully called. Completion rates were similar for buffy coat and buccal cell samples (99.63% and 99.44%, respectively; P = 0.15). Completion rates <99% were observed in only four samples and did not differ by specimen type. The paired samples showed exceptionally high concordance (99.96%). These results show that buccal cell samples collected and processed under optimal conditions can be used for genome-wide association studies with results comparable to those obtained from DNA extracted from buffy coat.