Reactive oxygen species (ROS) are molecules produced by reactions of partial oxygen degeneration and are characterized by high oxidative potential. ROS in a cell are usually generated by external factors or as a product of mitochondrial metabolism. The condition in which more ROS are produced than scavenged is called oxydative stress. Although a high level of ROS is damaging for cells and is linked to many pathological conditions, ROS play a crucial role in cell signaling pathways and are necessary for maintaining homeostasis. One of the ways how a cell defends itself from oxidative stress is the antioxidant enzyme system. Some of the most important enzymes of this system are catalase (CAT) and superoxide dismutase (SOD). Recent researches have been focusing on the circadian regulation of ROS levels even though the molecular mechanism of interaction between the circadian genes and the antioxidant enzyme system is still not fully understood. In the conducted experiment we investigated the impact that circadian genes have on the level of ROS using a model organism D.melanogaster, indirectly, by measuring the activity of CAT and SOD in wild type flies and different circadian mutants (per01,tim01,ClkJrk and cyc01). We have compared the activity of those enzymes during different times of the day and the difference between bodies and heads of flies. We found that the expression of genes coding for antioxidant enzymes were affected by the time of the day and regulated by the circadian clock. Furthermore, there was a notable difference between CAT and SOD activity in heads and bodies of the flies, thus confirming the existence of partial regulatory autonomy of peripheral tissues compared to the central regulatory clock in suprachiasmatic nucleus (SCN). Differences between the mutants were also significant.