An electronic article surveillance system (100) includes a signal generator (22, 24, 26) for generating an interrogation signal (28) in an interrogation zone (30), an antenna (36) which receives a signal (34) present in the interrogation zone (30), and circuitry for cancelling interference. A hybrid interference component cancelling loop forms a digital interference estimate signal (108) which is converted (106) into an analog estimate signal, which is subtracted (102) from an input analog signal (40). The difference signal is digitized and subjected to additional digital interference cancellation processes (108). Each of the signal processing operations (108) entails performing a polyphase decomposition of a digital input signal, estimating a mean value of each of the resulting subsequences, and combining the estimated mean values to form an interference component estimate signal. An input sample window for a comb-filtering stage is phase adjusted relative to the interrogation signal to compensate for changes in phase of the marker signal (34).