It is commonly observed that 'tone deaf' individuals are unable to hear the beat of a tune, yet deficits on simple timing tests have not been found. In this study, we investigated rhythm processing in nine individuals with congenital amusia ('tone deafness') and nine controls. Participants were presented with pairs of 5-note sequences, and were required to detect the presence of a lengthened interval. In different conditions the sound sequences were presented isochronously or in an integer-ratio rhythm, and these were either monotonic or varied randomly in pitch. It was found that the 'tone deaf' participants exhibited inferior rhythm analysis for the sequences that varied in pitch compared to those that did not, whereas the controls obtained equivalent thresholds for these two conditions. These results suggest that the rhythm deficits in congenital amusia result from the pitch-variations in music.