A method and system for continually monitoring oxygenation levels in real-timein compartments of an animal limb, such as in a human leg or a human thigh or a forearm,can be used to assist in the diagnosis of a compartment syndrome. The method andsystem can include one or more near infrared compartment sensors in which eachsensor can be provided with a compartment alignment mechanism and a central scandepth marker so that each sensor may be precisely positioned over a compartmentof a living organism. The method and system can include a device for displayingoxygenation levels corresponding to respective compartment sensors that aremeasuring oxygenation levels of a compartment of interest. The method and systemcan also monitor the relationship between blood pressure and oxygenation levelsand activate alarms based on predetermined conditions relating to the oxygenationlevels or blood pressure or both.