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Chicken infectious anaemia (CIA) and marek's disease (MD) are highly prevalent immunosuppressive viral infections in India and so natural co-infection is also likely to occur. The present study evaluated the extend of apoptosis induced in the thymocytes of SPF chicks challenged with CIAV and MDV both alone and in combination. Seventy two (72) SPF chicks were randomly allocated into 4 groups viz., CIAV (challenged with CIAV on day1), MD (challenged with vMDV on day14), CIAV + MD (challenged with CIAV on day1 and vMDV on day14) and CONTROL (without virus challenge). Three birds from each group were sacrificed on day14, 28 and 42, followed by collection of thymus and thymocytes were separated and suspended in PBS as single cell suspension. Further treatment of cells to release caspase3 and its colorimetric evaluation were done using caspACE assay kit (Promega). Results of present study indicated a significantly higher (p<0.05) level of caspase3 released in CIAV and CIAV + MD groups from day 14 onwards, reached peak on day 28 but by day 42 CIAV alone group showed a decline while in co-infected group the level remained significantly higher (p<0.05). So results of this study point to a greater extend of apoptosis in co-infected group, aggravating the immunosuppression.