Because of mathematica constraints I have to make use of the BigInteger class to represent values.

After a little information I must keep result (distributed by 2x BigInteger instances) into Mysql...

What's the best datatype to keep such object ?

I believed about utilizing a Blob to keep the binary format of individuals results (128 bits) ? But I must avoid unnecessary type conversions.

I would suggest utilizing a Blob and so the BigInteger(byte[] val) constructor to visit from byte array to BigInteger, and also the BigInteger#toByteArray() way of another way.

MySQL includes a BIGINT data type as proven in: http://dev.mysql.com/doc/refman/5.0/en/numeric-types.html

You can test to make use of the BIGINT for your instead of doing conversion to binary formats which causes it to be good deal more complicated to my estimation.