Mbagathi hospital, initially known as South Hill Hospital for Infectious Diseases was commissioned by Sir Fredrick Crawford in 1956.It opened its doors to its first patient for isolation as an extension of the current Kenyatta National Hospital, formerly known as the King George VI Hospital. The targeted diseases for isolation included Tuberculosis, Measles, Cholera, Diarrheal Epidemics, Leprosy, Meningitis, Plague among others. For a long time Mbagathi was popularly known as Infectious Diseases Hospital (IDH). The bed capacity has since grown from 266 to the current 320.

The hospital is a referral facility for Nairobi Metropolis catchment area. The average daily outpatient workload is about 1000 patients, with an inpatient bed occupancy of 200%. The hospital offers 24-hour services which include: Medical, Surgical, Rehabilitative, Diagnostic and Mortuary services.