Objective: The aim of this study was to explore the impact of automated hotspot detection on surgical planning of 18FET PET-guided stereotactic serial biopsy. Method: Imaging of ten patients with brain lesions detected by MRI and showing increased 18FET uptake on PET who were retrospectively and randomly assigned to compose the study. Stereotactic biopsy plans (PET-guided and MR-guided) were performed by two neurosurgeons for each patient, independently and blinded. For PET-guided plans, biopsy target was achieved by means of an automated hotspot detection system. MR-guided plans targeted contrast enhancement areas or hyperintense areas in T2-weighted sequences. FET uptake ratio (UR) was determined in the biopsy trajectory across the lesion. Highest UR (HUR) from both planning techniques was compared. Results: Each single HUR obtained through PET-guided technique was higher than correspondent values from MR-guided technique. Mean HUR of 2.41 (SE ± 0.23) for PET-guided plans and 1.85 (±0.16) for MR-guided plans were respectively obtained. This difference was statistically significant (p = 0.002). Conclusion: The use of an automated hotspot detection system was able to provide higher FET HUR along stereotactic biopsy trajectories in comparison to those from MR-guided plans. The use of specially designed computational tools may refine surgical planning by improving biopsy targeting.