If your data comes from a double blind , controlled experiment, the independent variables are exogenous. In this type of study, the only thing that affects the independent variables is you, the researcher–and you are outside the system. In other studies, the independent variables may be exogenous, or they may be endogenous. If they are endogenous, it means that some other variables within the system (perhaps another independent variable, or a confounding variable ) are affecting the results. This can have negative consequences on your results, which is why it’s important to have controlled experiments whenever possible.
When biologists need to make a distinction between things that are produced within a cell or organ and things that affect it from the outside, they use the terms endogenous and exogenous . It used to be thought, for instance, that mutations in cells always resulted from exogenous causes, until it was discovered that substances in the body, including those called oxidants, could cause them endogenously as well. "Circadian rhythms"—the regular cycles, roughly 24 hours in length, that plants, animals, and humans rely on to regulate their days—are endogenously generated and don't actually depend on the sun for their timing.