The use of chemical products has been a usual practice to reduce the incidence of soil-borne plant pathogens in both field and greenhouses. However, the application of chemicals causes soil and water contamination and severely reduces the diversity of the microflora in the treated soil. Therefore, finding alternative methods for controlling soil-borne plant pathogens has become essential for Agriculture and Horticulture in the future. Some of these alternatives are the use of tolerant cultivars, the employment of adequate management strategies and the development of biological methods. Among the possible appropriate cultural activities adequate irrigation, soil solarization, biofumigation, crop rotation and application of soil amendments should be taken into account. Biological methods would include the use - alone or combined - of antagonistic bacteria, fungal root endophytes, arbuscular mycorrhizal fungi (AMF), yeasts, viruses and soil fauna. The efficacy, possible problems and limitations of the application of biological agents to control soil-borne pathogens in different crop and ornamental plants are discussed in this review.