The paper provides the design method of portable fingerprint based attendance system using GSM. The system includes terminal fingerprint acquisition module and attendance module. It can realize automatically such functions as information acquisition of fingerprint, processing, and wireless transmission, fingerprint matching and making an attendance report. After taking the attendance, this system sends the attendance of every student to their parent’s mobile through GSM. Attendance system facilitates access to the attendance of a particular student in a particular case. This system eliminates the need for stationary materials and personnel for keeping of the records. To improve the accuracy of fingerprint identification system for implementation of large data bases for e.g.:- of an institute or a country etc. This paper have many new algorithms have been used by example gender estimation, key based one to many matching. Using these new algorithms, Developed an identification system which is faster in implementation than any other available today in the market. Although this fingerprint identification system for student identification purpose in this paper, the matching results are so good that it could perform very well on large data-bases.