This study reports the association of five blood types, three enzymes, two proteins, Escherichia coli F18 receptor gene (ECF18R), and the Ryanodin receptor (RYR1) gene with six production traits, four meat quality traits, and two osteochondral diseases in Swiss pig populations. Data on on-farm traits (daily weight gain, percent premium cuts, and backfat) and on station-tested traits (daily weight gain, feed conversion ratio, meat quality, and osteochondral lesions) were available on 3,918 and 303 animals, respectively. A mixed linear model with allele substitution effects was used for each trait by marker analysis (144 analyses). Significant marker-trait associations and allele substitution effects are presented. In general, heritability estimates for production and meat quality traits were higher than those for osteochondral lesions. Blood types lack significant associations with many traits except H and S types. Enzymes (mainly, glucose phosphate isomerase) and protein polymorphisms show significant associations with daily weight gain, premium cuts, and backfat as well as osteochondral lesions. The RYR and ECF18R genes significantly affected all growth, production, and lean meat content traits and osteochondral lesions; RYR also affected pH values. This study reports many novel marker-trait associations, particularly between the incidence of osteochondral lesions and polymorphisms at glucose phosphate isomerase, 6-phosphogluconate dehydrogenase, postalbumin 1A, RYR, and ECF18R loci. These results should be useful in selection and for further functional genomics and proteomics investigations.