A prospective population-based molecular and conventional epidemiological study of 65.4% of bacteriologically confirmed cases of tuberculosis was carried out on the island of Hong Kong from May 1999 to Oct 2000 by the IS6110-based restriction fragment length polymorphism technique. Eleven of the isolates had five or fewer bands; 24.5% of the remaining 691 isolates belonged to clusters. The estimated proportion of recently transmitted disease was 15 to 20%.