Plants dispense localised and systemic defense responses against biotic colonisers and plant resistance to pathogens depends upon timely recognition of pathogen infection and subsequent rapid activation of defense responses through signal transduction pathways. Induction of host defense responses involving compatible and incompatible interactions in tomato landrace, LE996, LE150 and LE1165 (Solanum lycopersicum), and wild relatives, Seijima Jeisei and I979 (S. hirsutum) genotypes, and early blight (EB) pathogen, Alternaria solani were studied. Accumulation patterns of different defense related proteins in resistant genotypes (LE996, Seijima jeisei and I979) and susceptible genotypes (LE150 and LE1165) are reported here. Challenge inoculation led to similar protein profiles in resistant genotypes yielding 11 proteins, unique are 14, 54, and 58 kD proteins that are absent with susceptible genotypes. Resistant genotypes accumulated more proteins well in advance, 6-h after challenge inoculation. Resistant genotype LE996 expressed 54%, 90%, and 52% enhanced enzymatic activity of peroxidase, polyphenol oxidase and phenylalanine ammonia lyase respectively than susceptible LE150 and correlated phenolics accumulation peaked 2-d after challenge inoculation. Activity gel assay indicated the unique expression of PO1 and PO2 in LE996 upon challenge inoculation. Significant increase in expression of chitinases (63%) and b-1,3-glucanase (71%) upon challenge inoculation than susceptible LE150 control was recorded. Western blotting indicated the unique presence of less than 30 kD chitinase in resistant LE996 and Seijima Jeisei and was absent in susceptible LE150. The results demonstrate the importance of pathogenesis-related (PR) proteins in EB resistance and their use as biochemical markers for genotype selection.