Research departments and the clinic are in the structure of the Institute. The "Science" division includes scientific-and-research and production departments. The scientific-and-research department consists of 3 departments: Corneal and Refractive Surgery; Reconstructive Eye Surgery in Children; Vitreoretinal and Laser Surgery. Scientific and production department includes a laboratory for the production of medical products, intraocular and contact lenses, Department for Foreign Relations and Marketing.

Currently, the Ufa Eye Research has a comprehensive clinical base completed with most-up-to-date operating units and excellent diagnostic equipment.

The Institute is composed of five Departments with 290 hospital beds (including department for children - 50 beds), Department of Hospital-Replacing Technologies, Outpatient Surgery Department, Adult and Children's Consultative Out-Patient Department, Laser Department, Department of Anesthesiology and Intensive Care, Functional diagnostics, Emergency Department with providing 24 hour emergency trauma care.