The cycle threshold is defined by the number or replication cycles it takes in a quantitative or real time PCR test for the value of a specific genetic sequence to rise in an exponential fashion above the baseline level. Typically PCR reactions used in medical diagnostics will typically run around 20 – 50 cycles. Higher initial levels of the targeted genetic material in the sample being tested, will give lead to an exponential rise in quantity of that genetic material in fewer cycles than if the target material was present in lower levels. This same phenomenon is also called the quantification cycle (Cq).

Counterintuitively, a lower cycle threshold implies that there was more of the target genetic material in the specimen.