OBJECTIVES: To determine the impact of rotavirus (RV) disease as a secondary diagnosis on hospital length of stay (LOS) and cost for children under five years of age in England. METHODS: The study was based on Hospital Episodes Statistics for England 2001-2007 using a matched cohort design. Admissions with a secondary diagnosis of RV were extracted and matched by age, year of admission and, where relevant, therapeutic procedure, to other admissions from HES with the same primary diagnosis.  Primary admissions were classified as potentially related or unrelated to RV. LOS was compared using the paired Wilcoxon test. RESULTS: Of 2126 admissions with a secondary diagnosis of RV, 707 (33.3%) had no other secondary diagnoses. Of these, 385 admissions were matched for primary diagnosis to controls. Median LOS for admissions was 2.0 days (Inter-Quartile Range [IQR] 1.0-4.0), mean (sd) 3.2 (4.1) compared with median 1.0 (IQR 0.0-1.5), mean 1.4 (sd 3.5) for control admissions (p-value <0.001). Median cost/admission was £771 (IQR £604-£1090), mean cost was £1105 (sd £1064) compared with median £650 (IQR £564-£1090), £902 (sd 1004) (p-value <0.001). A total of254/385 admissions were defined as unrelated to RV. For these admissions, median LOS was 2.0 days (IQR 1.0-4.25), mean 3.7 (sd 4.5) compared with median 1.0 (IQR 0.0-2.0), mean 1.6 (sd 4.0) for control admissions (p-value <0.001). Median cost/admission was £918 (IQR £564—£1090), mean £1132, (sd £1132) compared with median £771 (IQR £564-£1090), mean £980 (sd £1187), (p-value <0.001). CONCLUSIONS: As a secondary diagnosis in HES, RV has a significant incremental impact on LOS and cost. Variations in testing and reporting of RV mean that HES data may significantly under represent the overall burden of RV disease. This implies that standard modelling methodologies may underestimate the true burden of RV disease in the context of health care acquired infection.