Abstract: A two dimensional electrophoresis apparatus which includes a first dimension electrophoresis box assembly which is connected to second dimension electrophoresis box assembly to provide two dimensional electrophoresis of proteins, peptides, DNA/RNA and related materials. The apparatus is designed for use in conducting two dimensional electrophoresis where isoelectric focusing is carried out in a first dimension to provide separation of samples based on charge followed by polyacrylamide gel electrophoresis as a second dimension wherein the sample bands resulting from the first dimension electrophoresis are separated according to mass. The apparatus may also be used in conducting other two dimensional electrophoresis procedures based on combinations of other gels.