An apparatus and method for generating an initial puncturing matrix from which a first sub-code is produced in a communication system. The apparatus includes a turbo encoder for generating information symbols and first and second parity symbols for an information bit stream and a sub-code generator for generating sub-codes from the information symbols and the first and second parity symbols using puncturing matrices. The method includes the steps of selecting a number of information symbols equal to a number of columns in the initial puncturing matrix from the information symbols output from the turbo encoder, if a difference between the number Ns of selected symbols in the initial puncturing matrix and the number of the columns in the initial puncturing matrix is equal to or greater than a number of component encoders in the turbo encoder, and selecting a number of first and second parity symbols equal to the difference.