Background Cerebrospinal fluid (CSF) leakage represents a major source of morbidity following microvascular decompression (MVD) surgery. The objective of this study was to retrospectively assess whether complete versus incomplete reconstruction of the suboccipital cranial defect influences the incidence of CSF leakage following MVD. Methods We reviewed the charts of 100 patients who consecutively underwent MVD for trigeminal neuralgia by two attending neurosurgeons between July 2004 and April 2010. Operative variables including incomplete or complete calvarial reconstruction, primary dural closure or dural closure with adjunct, and use of lumbar drainage were recorded. The effect of complete calvarial reconstruction on the incidence of postoperative CSF leakage was examined using a multivariate logistic regression model. Results Of the 36 patients whose wound closure was reconstructed with a complete cranioplasty, 2 (5.6%) patients experienced a postoperative CSF leak. Of the 64 patients whose wound closure was augmented with an incomplete cranioplasty, 15 (23.4%) experienced a postoperative CSF leak. There was suggestive but inconclusive evidence that the risk of CSF leakage following MVD was smaller with complete reconstruction of calvarial defect than with incomplete reconstruction (two-sided p value = 0.059), after accounting for age, dural closure method, use of lumbar drainage, and previous MVD. Conclusion Complete reconstruction of the suboccipital cranial defect decreases the risk of CSF leakage.