Stone fruits orchards from three Chilean regions were visited to collect leaf samples which were tested for the presence of the most important viruses and viroids. Molecular nonradioactive hybridization (MH) testing of 2,456 samples and confirmatory RT-PCR of some MH-negative samples gave the following infection rates: 31.5% for Prunus necrotic ringspot virus (PNRSV); 31.3% for Prune dwarf virus (PDV); 25.7% for Peach latent mosaic viroid (PLMVd); 3.1% for Tomato ringspot virus (ToRSV) only in rootstocks; 1.8% for Plum pox virus (PPV); 1.2% for Hop stunt viroid (HSVd); 1.1% for Apple mosaic virus (ApMV); and 0.9% for Apple chlorotic leaf spot virus (ACLSV). American plum line pattern virus (APLPV) was not detected. The overall infection rate in the surveyed orchards was 29.6%, specifically 28.2% (Region Metropolitana), 23.4% (Valparaiso) and 33% (Bernardo O'Higgins) in the three regions surveyed. ApMV and HSVd, detected only in peach and nectarine, are new records in stone fruits in Chile.