Burkholderia cepacia was identified in samples of onion bulbs, rhizosphere,  field soil and storage debris from two different commercial onion production locations at Dakahlia and Gharbia governorates. Percentage of healthy onion bulbs with average of 85-89% was reduced gradually by the end of storage period after harvest to 59-64% in the end of storage period at the two storage locations, respectively. Data indicated that percentage of onion bulb scales with internal and external bacterial soft rot was minimum after harvest (0-2%) at early spring and increased gradually during summer to reach maximum infection (19 -22%) by the end of the summer at the two storage locations, respectively. Symptoms of bacterial rot include a breakdown of one or more inner bulb scales, while adjacent outer scales and inner portions of the bulb may remain intact. Rotten onion scales appear pale yellow, reddish-brown to a darker brown decay. Frequency of B. cepacia colonies detected in rhizosphere increased in rhizosphere of onion plants at mature bulbs stage (10^-6 X 4.8 and 10^-6 X 5.1 cfu/g) compared with rhizosphere of onion immature bulb stage (10^-6 X 1.9 and 10^-6 X 2.6 cfu/ g) in the two locations, respectively. The recovery of the B. cepacia colonies from onion storage debris was higher than any source of onion infection assayed in this study (10^-7 X3.4 cfu/ g). Physiological and biochemical tests showed that onion isolates were gram-negative, rod-shaped with rounded ends, had a few polar flagella and non spore-forming. All the positive isolates accumulated poly-p-hydroxybutyrate, not synthesizing arginine dihydrolase, produced oxidase, not fluorescence, grew at a temperature of +41°C and caused the rot of potato tubers, but did not affect the tobacco leaves. Number of detected and confirmed as B. cepacia was 69 isolates from Trypan blue tetracycline (TB-T) medium and 43 isolates from Azelaic acid tryptamine (PCAT) medium. B. cepacia was recovered more efficiently on TB-T medium than PCAT medium.  Pathogenicity of total 125, 75, 30 and 62 isolates from onion rhizosphere, field soil, bulb onion scales and storage debris, respectively showed that percent area of macerated scales tissue after inoculation and incubation at 30°C for 48h was estimated and a rating of 0 to 3 scale. The large majority of isolates tested were highly virulent, with pathogenicity ratings of 2- 3 indicating higher number of isolates maceration of the onion bulb tissue by 25 (83%) isolates from onion bulb scales followed by isolates from onion rhizosphere (32%) and 24% of isolates from onion storage debris.