We have designed and implemented a computer-based system for three-dimensional stereotactic planning of minimally invasive neurosurgical procedures. The system integrates rapid acquisition of digital medical images, segmentation, multi-modality registration, and three-dimensional planning capabilities. Emphasis on real-time planning is central to our system: imaging, pre-processing and planning are performed on the morning of surgery in clinically useful times. We have tested the system on procedures such as needle biopsies, depth electrode placements, pallidotomies, thalamotomies and craniectomies for arteriovenous malformations, aneurysms and tumors. We describe in this paper the core algorithms of our system, and discuss issues related to implementation, validation and user acceptance