Although only recently directional leads have proven their potential to compensate for sub-optimally placed electrodes, optimal lead positioning remains the most critical factor in determining Deep Brain Stimulation (DBS) outcome. Pneumocephalus is a recognized source of error, but the factors that contribute to its formation are still a matter of debate. Among these, operative time is one of the most controversial. Because cases of DBS performed with Microelectrode Recordings (MER) are affected by an increase in surgical length, it is useful to analyze whether MER places patients at risk for increased intracranial air entry. Data of 94 patients from two different institutes who underwent DBS for different neurologic and psychiatric conditions were analyzed for the presence of postoperative pneumocephalus. Operative time and use of MER, as well as other potential risk factors for pneumocephalus (age, awake vs. asleep surgery, number of MER passages, burr hole size, target and unilateral vs. bilateral implants) were examined. Mann-WhitneyUand Kruskal-Wallis tests were utilized to compare intracranial air distributions across groups of categorical variables. Partial correlations were used to assess the association between time and volume. A generalized linear model was created to predict the effects of time and MER on the volume of intracranial air, controlling for other potential risk factors identified: age, number of MER passages, awake vs. asleep surgery, burr hole size, target, unilateral vs. bilateral surgery. Significantly different distributions of air volume were noted between different targets, unilateral vs. bilateral implants, and number of MER trajectories. Patients undergoing DBS with MER did not present a significant increase in pneumocephalus compared to patients operated without (p = 0.067). No significant correlation was found between pneumocephalus and time. Using multivariate analysis, unilateral implants exhibited lower volumes of pneumocephalus (p = 0.002). Two specific targets exhibited significantly different volumes of pneumocephalus: the bed nucleus of the stria terminalis with lower volumes (p < 0.001) and the posterior hypothalamus with higher volumes (p = 0.011). MER, time, and other parameters analyzed failed to reach statistical significance. Operative time and use of intraoperative MER are not significant predictors of pneumocephalus during DBS. Air entry is greater for bilateral surgeries and may be also influenced by the specific stimulated target.