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The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species. DOI: http://dx.doi.org/10.7554/eLife.24232.001, eLife digest Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa. After the discovery was reported, a number of questions still remained. These questions included: why were so many fossils from a single species found at the one site, and how did they come to rest so far into the cave system? Possible explanations such as H. naledi living in the cave or being washed in by a flood were considered but ruled out. Instead, the evidence was largely consistent with intact bodies being deliberately disposed of in the cave and then decomposing. Now, Hawks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that yet more H. naledi fossils have been unearthed from a second chamber in the Rising Star cave system, the Lesedi Chamber. The chamber is 30 meters below the surface and there is no direct route between it and the Dinaledi Chamber. Again, the evidence is most consistent with the bodies arriving intact into the chamber, and there were no signs that the remains had been exposed to the surface environment. Also like the Dinaledi Chamber, no remains of other ancient humans or their relatives were found in the Lesedi Chamber. In total, 133 fossils of H. naledi have been found in this second chamber representing at least three individuals: two adults and a juvenile. However, and as Hawks et al. point out, only a small volume of the chamber has been excavated so far, and so there are likely more fossils still to be found. The fossils in the Lesedi Chamber are similar to those found before but include intact examples of bones, like the collarbone, that were previously known only from fragments. Perhaps the most impressive among the new fossils is a relatively complete skull that is part of a partial skeleton. The skull could have housed a brain that was 9% larger than the maximum estimate calculated from the previous H. naledi fossils. Though these new fossils provide us with yet more information about H. naledi, some questions still remain unanswered – the material from the Lesedi Chamber is undated, for example. However, a related study by Dirks et al. does give an estimate for the age of the fossils from the Dinaledi Chamber, while Berger et al. provide an explanation for why this date might be much younger than was previously predicted. DOI: http://dx.doi.org/10.7554/eLife.24232.002