Bats play a key role as reservoir hosts of many emerging viral diseases with zoonotic potential. However, little is known about the laboratory reference intervals (RIs) of bats, especially Egyptian fruit bats ( Rousettus aegyptiacus). The aim of this study was to obtain haematological, biochemical and electrophoretic RIs from captive fruit bats. Blood was collected from 21 R. aegyptiacus (11 females and 10 males). Complete blood cell count was performed using an impedance cell counter followed by the morphologic analysis of blood smears. Clinical biochemistry was performed with an automated spectrophotometer and agarose gel electrophoresis was carried out with an automated instrument. Reference intervals were determined using the Reference Value Advisor V2.1, following the American Society for Veterinary Clinical Pathology guidelines. Possible differences related to sex or sexual maturity were also investigated. The RIs for most of the analytes investigated were similar to those of other types of bats and other mammalian species. Haematology revealed mild polychromasia and slightly lower haematocrit, haemoglobin, leukocyte and lymphocyte counts compared to other bats. Glucose levels varied possibly due to stress, the anaesthetic protocol and fasting time. Creatine kinase was higher, while triglycerides were lower compared with domestic mammals and other bats. No sex- or age-related differences were found. Serum protein electrophoresis showed five fractions (albumin, α-, β1-, β2- and γ-globulins). The values recorded in this study could be helpful as a reference biological dataset to monitor the health status of wild and captive R. aegyptiacus and, possibly, of other Chiroptera.