One hundred forty serogroup Y Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease (IMD) in Canada from 1999 to 2003 were analyzed by genetic and serological methods. Seventy-four isolates (52.9%) belonged to serotype 2c, and most have serosubtype antigen P1.5,2 (37 isolates, 26%) or P1.5 (31 isolates, 22%). Forty-eight isolates (34.3%) belonged to serotype 14 and have serosubtype antigen P1.5,2 (13 isolates, 9%) or P1.5 (7 isolates, 5%) or were nonserosubtypeable (27 isolates, 19%). Thirteen isolates (9.3%) were nonserotypeable. Multilocus sequence typing identified two unrelated clonal populations of serogroup Y meningococci causing invasive disease in Canada: ST-23 and ST-167 clonal complexes. Almost all ST-167-related isolates were typed as 2c:P1.5, while strains of the ST-23 clonal complex were either serotype 14 or 2c but with the serosubtype antigen P1.5,2. In contrast to previous reports that patients with serogroup Y disease are usually older, 26% of the Canadian serogroup Y cases were found in the 10-to-19-year-old age group and another 11% were in the 20-to-39-year-old age group.