Background: Estimating multimorbidity (presence of two or more chronic conditions) using administrative data is becoming increasingly common. We investigated (1) the concordance of identification of chronic conditions and multimorbidity using self-report survey and administrative datasets; (2) characteristics of people with multimorbidity ascertained using different data sources; and (3) whether the same individuals are classified as multimorbid using different data sources. Methods: Baseline survey data for 90,352 participants of the 45 and Up Study—a cohort study of residents of New South Wales, Australia, aged 45 years and over—were linked to prior two-year pharmaceutical claims and hospital admission records. Concordance of eight self-report chronic conditions (reference) with claims and hospital data were examined using sensitivity (Sn), positive predictive value (PPV), and kappa (κ).The characteristics of people classified as multimorbid were compared using logistic regression modelling. Results: Agreement was found to be highest for diabetes in both hospital and claims data (κ = 0.79, 0.78; Sn = 79%, 72%; PPV = 86%, 90%). The prevalence of multimorbidity was highest using self-report data (37.4%), followed by claims data (36.1%) and hospital data (19.3%). Combining all three datasets identified a total of 46 683 (52%) people with multimorbidity, with half of these identified using a single dataset only, and up to 20% identified on all three datasets. Characteristics of persons with and without multimorbidity were generally similar. However, the age gradient was more pronounced and people speaking a language other than English at home were more likely to be identified as multimorbid by administrative data. Conclusions: Different individuals, with different combinations of conditions, are identified as multimorbid when different data sources are used. As such, caution should be applied when ascertaining morbidity from a single data source as the agreement between self-report and administrative data is generally poor. Future multimorbidity research exploring specific disease combinations and clusters of diseases that commonly co-occur, rather than a simple disease count, is likely to provide more useful insights into the complex care needs of individuals with multiple chronic conditions.