Summary: Today, is a world of uncertainty with its associated problems, which can well be handled by soft set theory, which is a new emerging mathematical tool. In this paper, we focus on developing an algorithm which is a new problem solving strategy in the medical diagnosis domain by implementing a novel term “intuitionistic fuzzy soft matrices”. In order to attain this, we define a value matrix and score matrix and the output is obtained, based on the maximum score in the score matrix.