This study was conducted to investigate the inhibitory effect of both extracts of and active ingredients in Allium plants on crop pathogens. Among Allium genus species, suppression rates of Pyricularia oryzae and Phytophthora cactorum were the highest when A. sativum flesh was used. In Allium species by-products, suppression of P. oryzae and P. cactorum was higher in A. sativum, A. wakegi and A. hookeri roots. In other pathogen tests, Colletotrichum coccodes was 94 and 86% suppressed in response to 5% concentrations of A. fistulosum root and A. sativum flesh water extracts, respectively. Additionally, Thanatephorus cucumeris was 95% suppressed in response to water extracts of A. sativum flesh at 5%. P. oryzae was 83% suppressed in response to quercetin at 3%. However, other pathogens P. cactorum, T. cucumeris, C. coccodes or Botrytis cinereal were only 29–47% suppressed in response to quercetin at 3%. The five pathogens were 74–100% suppressed in response to ascorbic acid at 3%. Furthermore, complete suppression of P. oryzae, C. coccodes and B. cinereal was achieved using allyl disulfide at concentrations of 0.1, 0.3 and 0.3%, respectively. The total thiosufinate contents were significantly different between some Allium species and cultivars. However, the suppression rates may not be attributed to any one single active ingredient. Thus, Allium plants and their by-products are useful in organic crop cultivation and may be used to control crop diseases.