Maybe the single most important reading that can be taken from a patient to truly measure their current physiological state is their expired CO2 measurement. This parameter plays an even more prevalent role in the administration of anesthesia. There are two ways to measure CO2 in clinical applications, 
Mainstream CO2
Mainstream CO2 is measured through the use of a sensor that is inserted via an airway adapter. The sample is taken directly from the airway. This method provides a very accurate reading because since the sensor is at the actual airway, there are far less variable involved that could interfere with an accurate 
Sidestream CO2
Sidestream CO2 uses a sensor that is located inside the monitor instead of an external sensor. For this method, the patient’s exhalation air is pulled through a small tube, usually 6-8’ long, from the sample site (usually a nasal cannula or a mask) and into the monitor. Usually the sample tube first will enter a water trap and/or filter which is attached to the monitor. The water trap is used to trap the heavier water vapor from entering the monitor, which can cause damage and errant readings.

Conclusion
Mainstream is widely regarded as the more accurate method of measuring CO2 readings. The disadvantage is the sensor, which is prone to being dropped or damaged and is quite expensive to replace. Industry advancements have made the sensor less vulnerable to damage, but the risk still exists.
Sidestream CO2 probably has less potential for major parts replacement because the sensor is internal. The readings may be less accurate because of the variables involved with pulling the sample from the patient to the monitor, then through a water trap, and into the internal sensor. Also, when using anesthetic agents, sidestream monitoring needs to have a scavenge system in place to divert the expired and sampled gas safely back into the anesthesia machine so that the room air during the procedure gets contaminated with expired anesthetic agent.
Both methods are acceptable for measuring CO2. Further research may indicate which method is more advantageous to utilize for your specific procedures and situations. The most important aspect may not be about whether the method is sidestream or mainstream, but that you are monitoring CO2.