A medical device treatment system configured to provide a flow of treatment gas through a medical device to at least disinfect a fluid pathway through the medical device, the system comprising: a treatment gas flow generator configured to generate a forced flow of treatment gas for delivery to the fluid pathway of the medical device; a gas circuit configured to conduct the forced flow of treatment gas from the treatment gas flow generator to the medical device comprising: a first interface configured to form a releasable sealed interface with a medical device fluid pathway inlet of the medical device such that the forced flow of treatment gas is directed into the fluid pathway of the medical device through the first interface; and a second interface configured to form a releasable sealed interface with a medical device fluid pathway outlet of the medical device such that the forced flow of treatment gas is received back into the gas circuit from the fluid pathway of the medical device through the second interface, wherein the medical device treatment system further comprises one or more sensors configured to generate one or more output signals conveying information related to the one or mote parameters of the forced flow of treatment gas, and one or more processors configured to execute computer program modules, the computer program modules comprising: a treatment timing module configured to determine a period of time during which treatment gas is directed through the fluid pathway of the medical device based on user input and/or one of (a) medical device parameters and (b) output signals generated by the one or more sensors; and a control module configured to control the forced flow of treatment gas based on one or more of user input, medical device parameters, and/or output information from the treatment timing module. a treatment gas flow generator configured to generate a forced flow of treatment gas for delivery to the fluid pathway of the medical device; a gas circuit configured to conduct the forced flow of treatment gas from the treatment gas flow generator to the medical device comprising: a first interface configured to form a releasable sealed interface with a medical device fluid pathway inlet of the medical device such that the forced flow of treatment gas is directed into the fluid pathway of the medical device through the first interface; and a second interface configured to form a releasable sealed interface with a medical device fluid pathway outlet of the medical device such that the forced flow of treatment gas is received back into the gas circuit from the fluid pathway of the medical device through the second interface, a first interface configured to form a releasable sealed interface with a medical device fluid pathway inlet of the medical device such that the forced flow of treatment gas is directed into the fluid pathway of the medical device through the first interface; and a second interface configured to form a releasable sealed interface with a medical device fluid pathway outlet of the medical device such that the forced flow of treatment gas is received back into the gas circuit from the fluid pathway of the medical device through the second interface, a treatment timing module configured to determine a period of time during which treatment gas is directed through the fluid pathway of the medical device based on user input and/or one of (a) medical device parameters and (b) output signals generated by the one or more sensors; and a control module configured to control the forced flow of treatment gas based on one or more of user input, medical device parameters, and/or output information from the treatment timing module.