Aim To use linked electronic medical and dental records to discover associations between periodontitis and medical conditions independent of a priori hypotheses. Materials and Methods This case-control study included 2475 patients who underwent dental treatment at the College of Dental Medicine at Columbia University and medical treatment at NewYork-Presbyterian Hospital. Our cases are patients who received periodontal treatment and our controls are patients who received dental maintenance but no periodontal treatment. Chi-square analysis was performed for medical treatment codes and logistic regression was used to adjust for confounders. Results Our method replicated several important periodontitis associations in a largely Hispanic population, including diabetes mellitus type I (OR=1.6, 95% CI 1.301.99, p<0.001) and type II (OR=1.4, 95% CI 1.221.67, p<0.001), hypertension (OR=1.2, 95% CI 1.101.37, p<0.001), hypercholesterolaemia (OR=1.2, 95% CI 1.071.38, p=0.004), hyperlipidaemia (OR=1.2, 95% CI 1.061.43, p=0.008) and conditions pertaining to pregnancy and childbirth (OR=2.9, 95% CI: 1.327.21, p=0.014). We also found a previously unreported association with benign prostatic hyperplasia (OR=1.5, 95% CI 1.052.10, p=0.026) after adjusting for age, gender, ethnicity, hypertension, diabetes, obesity, lipid and circulatory system conditions, alcohol and tobacco abuse. Conclusions This study contributes a high-throughput method for associating periodontitis with systemic diseases using linked electronic records.