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.