The 5 apple viruses, apple chlorotic leaf spot virus (ACLSV), apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple mosaic virus (ApMV) and prunus necrotic ring spot virus (PNRSV) and 1 viroid, apple scar skin viroid (ASSVd) are known major viral/viroid pathogens of apple in India. For identification of virus-free elite mother plants, 267 proposed mother plants from Trans-Himalayan region of India were indexed through DAS-ELISA and RT-PCR. Only 20% plants showed typical symptoms of virus/viroid, where as indexing though DAS-ELISA and RT-PCR revealed that, about 95% of apple plants were found infected with the virus/viroid. ASPV was most prevalent virus with 74.91% incidence followed by ACLSV (73.41%), ASGV (45.32%), PNRSV (1.5%) and ApMV (1.5%). Whereas, incidence of ASSVd was 2.62%. In the present study, it was recorded that 24.71% proposed mother plants were infected with a single virus, 38.95% with at least 2 viruses and 31.46% with more than 3 viruses. Only 4.86% plants out of 267 proposed mother plants were found free from virus/viroid infection. For sustainable supply of quality planting material, these virus free elite mother plants were multiplied and distributed to the farmers for establishment of mother blocks.