Disease reaction of three eggplant varieties (BAUBegun-1, BAUBegun-2 and Dohazari G) to collar rot (Sclerotium rolfsii) at early flowering stage, as well as the anatomy and biochemical effects of the infection on the collar region of the plant was studied. The plants were inoculated following soil inoculation technique, using barley culture of the pathogen. All the varieties were infected, with percentage infection ranging from 62.50 to 100%. Varieties varied in percent mortality (0.00 - 100). Plants of the eggplant variety BAUBegun-2, although infected, all regenerated and were graded resistant. The varieties Dohazari G and BAUBegun-1 were graded as susceptible. Anatomy and biochemical constituents, namely total phenols, ascorbic acid, total sugar, reducing sugar and Ca-oxalate contents of the collar region were investigated. BAUBegun-2 was characterized with thick cuticle, thick epidermal cells, many trichomes and smaller intercellular spaces in the cortex which could have restricted the entry of S. rolfsii into the cell. A higher level of biochemical activities was observed in eggplant var. BAUBegun-2. There was a clear correlation between anatomical features and biochemical constituents, and collar rot incidence. Anatomical features and biochemical constituents, as detected to be responsible for the resistance, could be used for the development of superior variety with resistance to collar rot.