OBJECTIVE To evaluate the feasibility, reliability and accuracy of the automated magnetic resonance spectroscopy ((1)H-MRS) guided frameless brain biopsy with intraoperative magnetic resonance imaging (iMRI). METHODS Between July 2011 and July 2013, a consecutive series of 93 patients were prospectively enrolled. All the patients had intracranial lesions which need biopsy to confirm the diagnosis. Among them, 48 patients were male, 45 patients were female. Their age range from 7 years to 76 years, the median age was 47 years. All patients underwent MRS examination. With MRS automatic fusion technique, the metabolic images were integrated into a standard navigation system (Vario Guide) to guide frameless biopsy. High-field iMRI (1.5 T) was used for target inspection, brain shift correction, and intra-operative exclusion of intra-cerebral hemorrhage and other complications. RESULTS For all the 93 patients, (1)H-MRS based metabolic images could be automatically integrated into a standard navigation system and average fusion procedure could be taken 5 minutes 6 seconds. For (1)H-MRS guided stereotactic biopsy of intracranial lesions, the diagnosis yield rate was 94.6% (88/93). Four cases did not get a clear pathological diagnosis, while 1 case did not match the pathological diagnosis result which obtained by following craniotomy. Technical related complication rate was 2.2% (2 cases, intra-cerebral hemorrhage), which were intra-operatively depicted with iMRI, and managed properly. Among them, 1 case with small volume (5 ml) intracerebral hematoma fully recovered 10 days after surgery without second surgical intervention. One case with large volume intracerebral hematoma (32 ml) was depicted with iMRI, followed by craniotomy and hematoma evacuation in the same session. This case had no new or worsened neurologic deficit post-operatively. CONCLUSIONS (1)H-MRS based metabolic imaging can be automatically integrated into a standard navigation system and used for frameless brain biopsy. The target can be selected according to the metabolic status of the lesion. Hence, the target can be more accurate. And the pathological diagnosis yield rate is higher. With iMRI, the method is safe, and has high clinical efficacy.