BACKGROUND: Documentation of diseases and intolerabilities in electronic patient records (EPRs) in pharmacies is needed to produce an alert in case a contraindicated medicine is prescribed. Limited research is available concerning EPRs in pharmacies. Objective: To study the prevalence and quality of documentation of diseases and intolerabilities in EPRs in a sample of Dutch community pharmacies. METHODS: Each participating pharmacy (N = 79) collected data on one day in May 2003 for each patient enrolled into the study (N = 687) concerning demographics, drug use, and documentation of diseases and intolerabilities. RESULTS: In 57.4% of the EPRs, at least one disease and, in 7.9%, at least one intolerability was documented. Higher age, number of drugs used, and chronic disease score were associated with any documentation of a disease/intolerability in the EPR. The highest sensitivity scores (completeness) were found for diabetes (84.7%), asthma/chronic obstructive pulmonary disease (strict definition: 75.9%), and hypothyroidism (75.0%). Rather low values were found for prostatic hyperplasia (55.6%) and heart failure (29.4%). The positive predictive value (reliability) was high for hypothyroidism (100%) and diabetes (87.1%). CONCLUSIONS: In a selection of Dutch pharmacies, at least one documented disease and/or intolerability was found in the EPR of almost 60% of the patients. Certain diseases were documented to a relatively high degree; others had poorer levels of documentation. For optimal surveillance of drug–disease interactions in pharmacies, the frequency and quality of disease and intolerability documentation need further improvement.