A 1-year cross-sectional study was carried out to determine the prevalence, risk factors for carriage, and genetic diversity of Campylobacter spp. in healthy dogs and cats in Switzerland. Veterinary practitioners collected samples from 1268 animals (all ages) presented for vaccination. The prevalence of Campylobacter spp. in 634 dogs and 596 cats that were eligible for the study was 41.2% (confidence interval 95%: 37.3–45.1%) and 41.9% (CI 95%: 37.9–46%), respectively. Risk factors identified for carriage of Campylobacter jejuni were found to be different from risk factors for C. upsaliensis/C. helveticus. Young animals (≤3 years) had significantly higher odds of carrying C. upsaliensis/C. helveticus than older animals (OR 1.8–3.3), whereas for C. jejuni carriage, the age was not a risk factor. Amplified fragment length polymorphism (AFLP) genotyping revealed heterogeneity among C. jejuni strains and was found to clearly separate C. helveticus from C. upsaliensis. It was shown that cats more often carry C. helveticus with an estimated prevalence of 28.2%, whereas dogs mainly are carrying C. upsaliensis.