Purpose To validate Covid-19 information records in The Pharmacoepidemiological Research Database for Public Health System (BIFAP), commonly used for pharmacoepidemiological research in Spain. Methods The recorded Covid-19 cases in primary care (PC) or positive test registries (gold-standard) were identified among vaccinated patients against SARS-CoV-2 infection of any age. They were matched with unvaccinated controls by birth year, vaccination date, region, and sex, between December 2020-October 2021. The sensitivity (SE), specificity (SP), positive (PPV), negative (NPV) predictive values, and date accurateness were estimated for PC by vaccination status and age brands. Results Among 21,702 patients with positive tests and 20,866 with recorded Covid-19 diagnoses, the SE, SP, PPV, and NPV were, respectively, 79.98%, 99.95%, 80.24% and 99.94% among vaccinated, and 78.67%, 99.96%, 84.51% and 99.94% among controls. For those aged ≥70 years old, SE (71.15-72.85%) was lower while PPV (84.68-88.04%) was higher compared to <70 years old participants. 94.12% of the total true positive cases (N=17,191) were recorded within ±5 days from the date of the test result. Conclusions PC Covid-19 diagnosis recorded in BIFAP showed high validation parameters. SE was similar and PPV was slightly lower among vaccinated than unvaccinated controls. Correction of vaccines effectiveness estimates by such misclassification is recommended. Data shows the influence of age. Among the elderly, Covid-19 diagnosis was less recorded but when recorded is more accurate than among younger patients. These findings permit the design of informed algorithms for performing Covid-19-related research.