Three deciduous tooth crowns were found in Unit 18B in El Castillo Cave (Spain), considered a transitional Middle-Upper Paleolithic Unit with numerous 14C dates with means earlier than > 42–44 ka cal. BP. Our goal was to describe these teeth, compare them to Neanderthal, Mousterian Modern Humans, and Early-Mid Upper Paleolithic fossils (through scatterplots and Z-scores), and analyze their morphology. The teeth consist of deciduous and isolated crowns (one ULdi1, one ULdm2, and one LRdm2) corresponding to three children, and all of them were modified by heavy occlusal and interproximal wear. Their length and breadth diameters, shown in the bivariate scatterplots, were similar to those of the teeth of several young Neanderthals. The Z-scores of the two crown diameters with respect to the Late Neanderthal, Qafzeh and Skhul, and Aurignacian-Gravettian series had values of approximately 0, while those of the altered MDs of the ULdm2 are just below − 1, except in comparison to the last group; the Z-scores of the BL diameters fall within the range of variability of the three series. Qualitative morphological comparisons highlighted several characteristics that were consistent with a Neanderthal taxonomic assignment. The combined archeological and anatomical-comparative study suggested the presence of three Neanderthal children in Unit 18, in a location considered a primary butchery area. The chronology and morphology of these teeth in the framework of the Middle to Upper Paleolithic transition are outstanding in the debate about the last Neanderthals and the unconfirmed, but possible, presence of a few groups of modern humans in Western Europe.