To determine prevalence, serotype diversity and antimicrobial resistance of Salmonella in healthy pigs, faecal samples from 6771 pigs on 73 farms collected during 1998-1999 and 2004-2005 were examined. Salmonella isolates were serotyped and tested for susceptibility to 22 antimicrobials: benzylpenicillin, ampicillin, amoxicillin, cefazolin, cephaloridine, gentamicin, kanamycin, streptomycin, fradiomycin, colistin, tetracycline, chlortetracycline, oxytetracycline, chloramphenicol, thiamphenicol, sulfadimethoxine, sulfamethoxazole, sulfamethoxypyridazine, trimethoprim, sulfamethoxazole/trimethoprim, norfloxacin and ofloxacin. Farm-level and pig-level Salmonella prevalences were 35.5% and 2.2% in 1998-1999, and 35.7% and 3.3% in 2004-2005. Prevalence by growth stage was 2.4% for sows, 3.3% for weaned pigs, 2.7% for fattening pigs and 3.8% for finishing pigs. The predominant serotypes identified were Agona (28.4%), Typhimurium (17.9%) and Infantis (16.4%) in 1998-1999, and Typhimurium (32.5%), Anatum (24.6%) and Infantis (13.5%) in 2004-2005. Compared with the 1998-1999 isolates, the 2004-2005 isolates showed significantly higher rates of resistance to all the antimicrobials except tetracyclines (P<0.01 to P<0.05) and resistance to 2 antimicrobials [19.4% (13/67) vs. 39.7% (50/126), P<0.01]. This study provides national estimates of Salmonella prevalence in healthy pigs of different growth stages in Japan.