Several different pathogens (fungi, fungi-like, bacteria, nematode, virus, and virus-like agents) can cause significant economic losses of blueberry, caneberry (raspberry and blackberry), strawberry, and other berry crops. Diseases caused by viruses and virus-like agents are incurable due to lack of effective pesticides. Infected nursery materials are means of introduction and disseminate of these pathogens due their systemic nature of infection. Therefore, nursery stocks shall be produced preventing the introduction and spread of all important systemic pathogens for berry orchards. Nursery stock certification programs are designed and implemented based on a system approach where critical components and standards are identified and integrated to produce healthy nursery stocks that are originated from a healthy mother source. This mother source has been tested and found free of target pathogens. Clean Plant Center-Berries tests, eliminates pathogens if infected, and maintains such mother source as G1 (Generation 1) materials. A G1 source is available to a nursery for further increase and multiplication. A nursery participating in a certification program, administered by the State Department of Agriculture, further increase and multiply this material as G2 (Generation 2) and G3 (Generation 3) as registered mother stocks in a pre-approved site. These registered stocks are used to produce certified nursery stocks (Generation 4, G4) for sale and distribution to berry growers. The Department of Agriculture administers, audits, tests, and implements certification standards and best management practices to maintain the G1 level cleanliness status while increasing G2 and G3 registered stocks and producing G4 certified stocks in a nursery site for berry growers.