Objectives: The Krapina rock shelter has yielded a large assemblage of early Neandertals. Although endocranial volume (ECV) has been estimated for four individuals from the site, several published values that appear in the literature warrant revisiting. Materials and Methods: We used virtual methods, including high-resolution surface models of fossils and 3D geometric morphometrics, to reconstruct endocasts and estimate ECV for five Krapina crania. We generated 10 reconstructions of each endocast to quantify missing data uncertainty. To assess the method and our ECV estimates, we applied these techniques to the Spy II Neandertal, and estimated ECV of a human reference endocast simulating the missing data of the Krapina fossils. Results: We obtained an average ECV estimate of 1,526 cm 3 for Spy II, consistent with previous research. Estimated ECV of juveniles Krapina 1 and 2 average 1,419 and 1,286 cm 3 , respectively. Estimates for the relatively complete adults Krapina 3 and 6 range from 1,247 to 1,310 cm 3 and 1,135 to 1,207 cm 3 , respectively, while the more fragmentary Krapina 5 averaged 1,397 cm 3. The missing data simulation suggests more fragmentary crania yield more uncertain and possibly overestimated ECVs. Conclusions: We have provided new estimates of brain size of the Krapina Neandertals, including the first estimates for Krapina 2. Brain size at Krapina was similar to other pre-Würm Neandertals, within the range of but lower than the average of later Neandertals. Although the virtual approach overcomes many challenges of fossil preservation, our results are nevertheless subject to future revision.