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Background and objectives Multiple brain lesions represent a serious challenge in which biopsy is commonly the first step to help overcome patients' mental anxiety and decide the following treatment step. This study presents an effective decisional algorithm that could guide in dealing with such a challenge. We evaluate the feasibility and safety of frame-based stereotactic biopsy to obtain the histopathologic diagnosis of the multiple intra-axial brain lesions and to decide the further treatment. Patients and methods Thirty-two patients with multiple intracerebral lesions underwent stereotactic serial biopsies for brain lesions at the Neurosurgery Department, Tanta University Hospital. All the stereotactic biopsies were obtained under local anesthesia using Riechert–Mundinger (RM) system or Cosman–Roberts–Wells (CRW) system. Results The histopathological diagnosis revealed multifocal malignant gliomas in 43.75% of patients (18.75% anaplastic astrocytoma and 25% multiform glioblastoma) and metastatic tumor in 37.5% of patients (all were adenocarcinoma). In addition, 12.5% had multiple brain abscesses, and 6.25% had malignant lymphoma. We reported no mortality secondary to the surgical procedure. Conclusions Stereotactic biopsy is considered the best choice to allow histopathologic diagnosis of multiple brain lesions with minimal morbidity and no mortality. Histopathologic findings gained with stereotactic procedures guided the choice of proper treatment thus eliminating the hazards associated with blind treatments.