Tuberculosis incidence in New York City (NYC) declined between 1992 and 2000 from 51.1 to 16.6 cases per 100,000 population. In January 2001, universal real-time genotyping of TB cases was implemented in NYC. Isolates from culture-confirmed tuberculosis cases from 2001 to 2003 were genotyped using IS6110 and spoligotype to describe the extent and factors associated with genotype clustering after declining TB incidence. Of 2408 (91.8%) genotyped case isolates, 873 (36.2%) had a pattern indistinguishable from that of another study period case, forming 212 clusters; 248 (28.4%) of the clustered cases had strains believed to have been widely transmitted during the epidemic years in the early 1990s in NYC. An estimated 27.4% (873 minus 212) of the 2408 cases were due to recent infection that progressed to active disease during the study period. Younger age, birth in the United States, homelessness, substance abuse and presence of TB symptoms were independently associated with greater odds of clustering.