The article presents a novel method for performing phenome-wide association scans (PheWAS) to discover gene-disease associations using International Classification of Disease (ICD9) billing codes from electronic medical records (EMRs). The authors developed a code translation table to define 776 disease populations and their controls using prevalent ICD9 codes. They genotyped the first 6005 European-Americans in the BioVU DNA biobank at five single nucleotide polymorphisms (SNPs) with previously reported disease associations. The PheWAS software generated cases and controls for each SNP across all ICD9 code groups, and the study replicated seven known SNP-disease associations with P-values between 2.8 × 10−6 and 0.011. Additionally, 19 previously unknown statistical associations were identified. The study demonstrates the feasibility of PheWAS as a method to investigate SNP-disease associations and highlights the potential for further evaluation to determine the validity and clinical significance of these associations. The PheWAS software and code translation table are freely available for use.The article presents a novel method for performing phenome-wide association scans (PheWAS) to discover gene-disease associations using International Classification of Disease (ICD9) billing codes from electronic medical records (EMRs). The authors developed a code translation table to define 776 disease populations and their controls using prevalent ICD9 codes. They genotyped the first 6005 European-Americans in the BioVU DNA biobank at five single nucleotide polymorphisms (SNPs) with previously reported disease associations. The PheWAS software generated cases and controls for each SNP across all ICD9 code groups, and the study replicated seven known SNP-disease associations with P-values between 2.8 × 10−6 and 0.011. Additionally, 19 previously unknown statistical associations were identified. The study demonstrates the feasibility of PheWAS as a method to investigate SNP-disease associations and highlights the potential for further evaluation to determine the validity and clinical significance of these associations. The PheWAS software and code translation table are freely available for use.