In this paper, we describe a system for the identification of the trajectory of a novel reciprocating drill for geological exploration. The entire system (drill + measurement system) must withstand the harsh environmental conditions typical of the deep underground inspections. The trajectory of the system is determined using the orientation with respect to the gravity (using two dual axis accelerometers) and with respect to the earth magnetic field (using a triaxial magnetometer). Performances of the trajectory measurement system have been studied using Monte Carlo simulations. The reliability of different algorithms for the identification of the trajectory is also discussed. Results of preliminary experiments performed on commercially available MEMS accelerometers evidenced the possibility of obtaining a position error in the order of tens of meters each 1000 m travelled.