Background: In Japan, a multiple-hospital observational database system, the Medical Information Database Network (MID-NET®), was launched for post-marketing drug safety assessments. These assessments will be based on datasets with missing laboratory results. The characteristics of missing data considering hospital differences have not been evaluated. We assessed the missing proportion and the association between missingness and a factor through case studies using a database system, a part of MID-NET®.Methods: Seven scenarios using laboratory results before the prescription of the assessed drug as baseline covariates and data from 10 hospitals of Tokushukai Medical Group were used. The missing proportion and the association between missingness and patient background were investigated per hospital. The associations were assessed using the log of adjusted odds ratio (log-aOR). Additionally, an ad hoc survey was conducted to explore other factors affecting the missingness.Results: For some laboratory tests, missing proportions varied among hospitals, such as 7.4%–44.4% of alkaline phosphatase (ALP) and 8.1%–31.2% of triglyceride (TG) among statin users. The association between missingness and affecting factors also differed among hospitals for some factors; example, the log-aOR of hospitalization associated with missingness of TG was -0.41 (95% CI, -1.06 to 0.24) in hospital 3 and 1.84 (95% CI, 1.34 to 2.34) in hospital 4. In the ad hoc survey focusing on ALP, hospital-dependent differences in the ordering system settings were observed.Conclusions: Hospital differences in missing data appeared in some laboratory tests in our multi-hospital observational database, which could be attributed to the affecting factors, including the patient background.