The aim of this study was to compare, by randomly amplified polymorphic DNA (RAPD), the diversity of Streptococcus suis serotypes 1/2 and 2 isolates recovered at slaughter houses from the tonsils of clinically healthy pigs. The pigs belonged to herds with or without clinical signs of S. suis disease. Overall, a low diversity was observed among isolates of serotype 1/2. A representative isolate recovered from a diseased animal presented a relatively high similarity (85%), with most isolates recovered from carrier pigs, from herds either with or without clinical signs of S. suis disease. For serotype 2 isolates, a relatively high degree of heterogeneity was observed in the whole population. Two subpopulations were observed for serotype 2 isolates, which arose from herds with clinical signs. Interestingly, the representative isolate coming from the diseased pig was included in a small closed cluster, with 2 isolates recovered from carrier pigs belonging to the same herd. On the other hand, most of the S. suis serotype 2 isolates originating from herds with no history of S. suis disease, were closely related (90% similarity). Furthermore, they presented different RAPD patterns from those originating from animals from the herd presenting S. suis clinical signs due to this serotype. Results suggest that, in the herds studied, clinical manifestations due to serotype 2 are probably related to the virulence of a specific isolate. Conversely, for the herd affected with serotype 1/2, clinical manifestations of the disease were more likely to be the result of inherent herd factors than the virulence of the specific isolate.