We describe a rapid method for subtyping Mycobacterium tuberculosis based on PCR amplification of segments located between two distinct DNA repetitive elements. This method, double-repetitive-element PCR, classified 46 clinical isolates as having 25 distinct patterns; the conventional restriction fragment length polymorphism analysis classified the same isolates as having 23 distinct patterns. The double-repetitive-element PCR is a rapid subtyping method that has a discriminating power similar to that of the restriction fragment length polymorphism method.