The Sima de los Huesos hominins are a 430,000 year old population of "pre-Neanderthals" from the archeological site of Atapuerca, Spain. They are in the "Neanderthal clade" but fall outside of Homo neanderthalensis. When first published in 1993, these 29 individuals represented about 80% of the human fossil record of the Middle Pleistocene. They preserve every bone in the human body, and the unprecedented completeness of the remains sheds light on Neanderthal evolution, the classification of contemporary fossils, and the range of variation that could exist in a single Middle Pleistocene population. Exhumation of the Sima de los Huesos hominins began in the 1980s, under the direction of Emiliano Aguirre and later Juan Luis Arsuaga, Eudald Carbonell, and José María Bermúdez de Castro.

As a pre-Neanderthal population, the Sima de los Huesos hominins display a mosaic of classic Neanderthal traits (apomorphies) as well as more archaic traits (plesiomorphies). Like in Neanderthals, the brow ridges are inflated, but the skull is not as robust in its rear and has a pointed "house-like" profile instead of the rounded "bomb-like" profile. Brain volume averages 1,241 cc (75.7 cu in), on the lower end of the Neanderthal range of variation. The teeth are Neanderthal-like, with shovel-shaped incisors and taurodontism, but differ in tooth cusp morphology. The chest and waist are broad and robust like in Neanderthals, but the limbs are longer. They may have been overall large-bodied like other archaic humans, with dimensions of about 170 cm (5 ft 7 in) and 90 kg (200 lb) for both males and females.

The Sima de los Huesos ("bone pit") is a chamber inside the Cueva Mayor – Cueva Silo cave complex at Atapuerca and may have been a natural trap that creatures fell into — especially the cave bear Ursus deningeri. The Sima de los Huesos hominins may have, instead, been intentionally deposited into the pit by other humans, based on the quality of preservation, and the predominance of adolescents and young adults over children and elderly (catastrophic mortality profile), who were all buried at about the same time. One individual may have been murdered with a blunt tool. Some individuals with severe health issues survived for quite some time, suggesting group care. Many individuals, especially adolescents, present several metabolic and malnutritional diseases altogether consistent with insufficient fat reserves during hibernation, which may have lasted four months.

This population was producing Acheulean stone tools, as well as an industry seemingly transitioning into the typically-Neanderthal Mousterian culture. They used these tools in butchering, as well as in hide- and woodworking in combination with the mouth as a third hand. The Sima de los Huesos hominins were buried with a single, large Acheulean handaxe, possibly a grave good with symbolic significance. Symbolic thought could indicate the use of an early form of language. They may have been efficient hunters — possibly outcompeting local cave hyenas — pursuing deer, rhinoceros, horse, bison, and (more sporadically) cave lion in an open woodland environment. They were likely eating roots regularly and habitually squatted. They probably were not using fire.

In 1868, Spanish engineers P. Sampayo and M. Zuaznávar published a monograph documenting the many caves in the Sierra de Atapuerca, noting reports of human fossils in one (Cueva Ciega). In 1910, Spanish archeologists Jesús Carballo García [es] and Saturio González discovered a cave painting of a horse in Cueva Mayor, and the area quickly generated international interest. The eventually-abandoned construction of a railway (which was supplied by material mined out of what became known as the Trinchera del Ferrocarril, "railway trench") revealed that the Cueva Mayor was part of a larger cave complex, the Cueva Mayor – Cueva Silo complex. Its archeological significance was first understood in 1962 after exploration by the Edelweiss Speleological Group, who identified several sites here strewn with Neolithic, Chalcolithic, and Bronze Age artifacts. While working on his doctoral thesis, Trinidad Torres unsuccessfully searched for bear fossils in the Trinchera del Ferrocarril but was pointed by the Edelweiss Spelaeological Group to the unmapped Sima de los Huesos ("bone pit") in the Cueva Mayor – Cueva Silo complex. Sampayo and Zuaznávar had marked this as El Silo ("storage pit"), a chamber down a 13 m (43 ft) vertical shaft in the corner of the spacious Sala de los Cíclopes.

Torres sent four speleologists who identified a wealth of cave bear fossils (Ursus deningeri), as well as a nearly complete human jaw fossil. He notified his PhD advisor, Emiliano Aguirre, who organized further digs. The Sima de los Huesos was difficult to access, low in oxygen, and had been disturbed by many visitors over decades looking for bear fossil trophies — requiring much more excavation to remove the disturbed sediments ("revuelto"). In 1983, Aguirre found three fossil human teeth (as well as more bear fossils) in his brief visit to the Sima de los Huesos. Removal of sediment began the following year after installing lights and other necessary infrastructure. In 1987, Aguirre's team installed suspended scaffolding over the floor of the Sima de los Huesos to walk on. Large sediment blocks were transported up the vertical shaft (the only entrance), carried out through the mouth of Cueva Mayor with backpacks, driven out to the nearby River Arlanzón, dried, sieved, and later sorted. The "Atapuerca Team" under Aguirre had reconstructed three crania, one of which was nicknamed "Lazarus" — the first fossil from the site given a nickname.

Aguirre retired in 1990, and left excavation in the hands of his three team leads: Juan Luis Arsuaga, Eudald Carbonell, and José María Bermúdez de Castro. In 1992, a nearly complete skull (nicknamed "Agamemnon") was found; at the time only three other European skulls predating the Late Pleistocene had come close to such a level of preservation (Swanscombe, Petralona, and Steinheim). Soon after, another nearly complete skull was discovered, nicknamed "Miguelón" after Spanish cyclist Miguel Indurain. It is one of the best preserved skulls in the human fossil record. In 1994, a nearly complete pelvis ("Elvis") was discovered; at this time, the only equivalently preserved hominin pelvis predating the Late Pleistocene was the 3.2 million year old "Lucy".

Since then, over 7,000 human fossils and fragments have been recovered from the Sima de los Huesos, representing every bone in the skeleton. The material was preliminarily thought to represent 32 individuals, but it more likely comprises 29. When first published in 1993, it was the most complete sample of the Middle Pleistocene human fossil record from a single site, representing 80% of the Middle Pleistocene human fossil record globally, and 85% of Middle Pleistocene postcranial (body) fossils. A similarly rich Middle Pleistocene human fossil assemblage was found in 2013, with the discovery of Homo naledi in South Africa. The Sima de los Huesos fossils elucidated the range of anatomical variation that could be present in any given population of Middle Pleistocene Europe — including across sex and age. Consequently, it clarified the relationships between Middle Pleistocene European fossils, as well as the evolution of Neanderthals. The great archeological significance of the Sima de los Huesos and other sites in the cave complex led to UNESCO declaring the archeological site of Atapuerca a World Heritage Site on 30 November 2000. To commemorate its cultural heritage, the city of Burgos about 12 km (7.5 mi) east opened the Museum of Human Evolution.