Disease tolerant/resistant onion (Allium cepa L. cv ADR and ALR) cell lines were selected against purple blotch disease caused by Alternaria porri. For this purpose callus and cell suspension cultures derived from mature embryos were exposed to purified toxic culture filtrate produced by the fungus supplemented with MS culture medium. Two selection methods were used: a continuous method in which four cycles of selection were performed on toxic medium whereas during discontinuous method, a pause was given after the second and third cycle of selection using non-toxic medium. Almost 4700 calli obtained from mature embryo and 8300 cell clumps from cell suspension cultures of two onion cultivars were exposed to media with phytotoxin for selection. The discontinuous method proved to be superior as it allowed the calli to regain their regeneration capability. Continuous exposure with toxic culture filtrate resulted up to 78% mortality. In vivo pathogenesity test of regenerated plants from the surviving tolerant/resistant cell lines revealed non-sensitive against pathogen toxin. A total 4 lines of ADR and 2 of ALR were documented resistant/tolerant amongst an array of putative resistant/tolerant lines during S1 generation.