Methods of testing a user design implemented in a programmable integrated circuit (IC). The programmable IC is programmed with a first test design that includes the user design and a first test circuit, and a first test pattern is run. The programmable IC is then programmed with a second test design that includes the user design and a second test circuit, and a second test pattern is run. If one of the test patterns fails and the other passes, the programmable IC passes the test sequence. Because one of the test patterns passed, the error in the other test pattern must have occurred in the test circuit, which is not necessary for the functioning of the user design in the programmable IC. Thus, the success of one test pattern shows that the flawed resource is not included in the portion of the programmable IC utilized for implementing the user design.