Background: The sterility mosaic disease in pigeon pea caused by pigeon pea sterility mosaic virus is a serious threat to pigeon pea cultivation in India. A little information is available on the biochemical changes in pigeon pea plant against the SMD disease. Hence present study was taken to know the biochemical alterations in different pigeon pea genotypes due to sterility mosaic disease. Methods: Studies were conducted on the composition of the chlorophyll pigment, total soluble protein (%), total sugars, phenol, tannins, peroxidase and phenol peroxidase in six different genotypes. Result: The results of the study showed that there was a reduction in chlorophyll pigment composition, total soluble protein (%) and total sugars in all infected genotypes, but the reduction in resistant genotypes was less compared to other genotypes. In resistant genotypes, the amounts of phenols, tannins, peroxidase and phenol peroxidase were increased, where as in susceptible genotypes, they were roughly equal to the amounts in uninoculated genotypes. The increase in phenols, tannins, peroxidase and phenol peroxidase in resistant genotypes can be correlated with disease resistance.