Infectious diseases are major burdens for the swine industry. Host genetics is an important factor in the outcome of host-pathogen interactions. Single-nucleotide variants in pigs were associated with the presence of common pathogens and infectious diseases via genome-wide association studies. In the first study, 461 cases diagnosed with diseases or pathogens and 1003 controls were investigated; the second study analyzed 40 cases diagnosed with Streptococcus suis disease and 23 controls from twelve farms. Data were analyzed using the genome-wide efficient mixed model association algorithm (GEMMA). In study one, a variant in AGAP1 was significantly associated with Salmonella Typhimurium(p<5.0×10-7). Variants in ATP2B1, DPYD, PID1, AGAP1, SNTB1, ACVRL1, NIFK, and MALL were suggestively associated with various bacterial and viral pathogens, and swine diseases(p<1.0×10-5). In study two, variants in PLEKHM1, LRRC37A, and WNT3 were suggestively associated with S. suis disease(p<1.0×10-5). These results may help breeding programs improve the robustness of pigs.