Lapa do Santo is an archaeological site located in the northern part of the Lagoa Santa karst, in the state of Minas Gerais in east-central Brazil. It documents human presence since ca. 8500 BC presenting three discrete occupation phases that correspond to the early, middle and late Holocene. Lithic technology, zooarchaeology, and multi-isotopic analyses indicate groups of hunter gathers with low mobility and a subsistence strategy focused on gathering plant foods and hunting small and mid-sized mammals. The use of Lapa do Santo as an interment ground started between 10.3 and 10.6 cal kyBP with primary burials. Between 9.6 and 9.4 cal kyBP, central elements in the treatment of the dead were tooth removal, mutilation, defleshing, exposure to fire and possibly cannibalism, all to reduce the body ahead of reburial of the remains while adhering to strict rules. In the absence of monumental architecture or grave goods, these groups were using parts of fresh corpses to elaborate their rituals. As part of this funerary agenda Lapa do Santo presents the oldest case in the New World of decapitation. Another type of burial included pits filled with separated bones of a single individuals presenting abundant evidence of perimortem fracturing. Lapa do Santo also presents a rare instance of securely dated rock art: an early Holocene low relief anthropomorphic figure depicting a phallus.

Lagoa Santa is located in east-central Brazil and is well known among archaeologist and paleontologists since the 19th century. The first human skeletons were found by the Danish naturalist Peter Lund between 1835 and 1844 in the Sumidouro cave in association with bones of extinct megafauna. Due to this putative coexistence of humans and megafauna, Lagoa Santa became the focus of many 19th century scholars. During the 20th century, different teams went to the region pursuing to find evidence that could confirm the coexistence hypothesis. As a result of more than 170 years of excavations, a large collection of early Holocene skeletons was formed. However, all those excavation were done in a time when proper documentation was not available and therefore they considerably lack contextual information. Coordinated by Prof. Walter Neves of University of São Paulo and funded by the São Paulo State Grant Foundation (FAPESP) the project "Origins and Microevolution of Man in America: a Paleoanthropological Approach" aimed to overcome this situation by identifying and excavating new sites in Lagoa Santa region. Excavations took place between 2001 and 2009 under the coordination of Renato Kipnis, Astolfo Gomes Melo Araujo and Danilo Bernardo. Starting in 2001, several units were open in distinct areas of the shelter. It became apparent that the densest archaeological deposits were located in the south part of the shelter, immediately in front of the cave's entrance. An ample excavation surface was established in this region becoming the Main Excavation Area (MEA). All human burials were found in the MEA. Excavations of the MEA ended in 2009 when, according to Brazilian laws, the excavated area was filled with sediments recomposing the original topography of the shelter's floor. In 2011, a new excavation area was open in Lapa do Santo as part of another research project. Entitled "The Mortuary Rituals of the First Americans" and coordinated by André Strauss and Rodrigo Elias Oliveira this was a joint venture between the Department of Human Evolution of the Max Planck Institute for Evolutionary Anthropology and the Institute of Biosciences of University of São Paulo.

"Lapa" and "Santo" are the Portuguese words for, "rockshelter" and "saint". Lapa do Santo is a cave with an associated sheltered area of ca. 1,300 m². The southern region of the sheltered area has a relatively flat, height and dry area located immediately in front of the cave's entrance. The floor of the shelter has a strong descending inclination towards the north, which becomes flat again near a natural sinkhole located at the northern extreme of the sheltered area.

A three-dimension coordinate system (x,y,z) was established in Lapa do Santo. The y-axis was conveniently oriented following the longer dimensions of the sheltered area, which is, in turn, roughly aligned with the geographic north–south axis (increasing towards the north). Therefore, the y-axis is also referred to as the north–south or N-S axis. The x-axis is perpendicular to the y-axis and is therefore roughly aligned with geographic east–west (increasing towards east). The x-axis is also referred to as the east–west or E-W axis. X-axis and y-axis define a horizontal plane. The z-axis is perpendicular to the plane defined by x-axis and y-axis and is therefore also referred to as the vertical axis or absolute depth (decreasing with progressive depth). The origin of the coordinate system (i.e. x=0, y=0, y=0) was conveniently positioned outside the sheltered area. An arbitrary grid with squares of 1 meter per side was established starting from the origin of the coordinate system. In the x-axis, each one-meter interval was sequentially labeled with letters (A,B,C,D, etc.) and in the y-axis, each one-meter interval was sequentially labeled with numbers (1, 2, 3, 4, 5, etc.). The excavation of the site followed this grid and the unit's code refers to this system (e.g. L11, B13, Z14).

Lapa do Santo is located in Lagoa Santa region, eastern central Brazil. Lagoa Santa is an environmentally protected area comprising 360 km². The vegetation is dominated by savanna (cerrado) and semi-deciduous forest. The rivers Mocambo, Samambaia, Jaguara and Gordura make up a tributary net that flows west to east to Velhas River, the main river in the area. Geomorphologically Lagoa Santa is a karstic terrain that can be divided into four distinct domains: 1) below 660 meters above sea level (masl) the terrain is characterized by a fluvial plain connected with the regional base level (Velhas River); 2) between 660 and 750 masl there is a karstic plain with dolines and lakes 3) between 750 and 850 masl there are karstic plateaus characterized by the presence of limestone outcrops (reaching up to 75 meters in height); 4) above 850 masl residual peaks composed of the non-soluble metasedimentary rocks from the Serra da Santa Helena Formation. The Lagoa Santa region geology comprises Sete Lagoas Formation and Serra da Santa Helena Formation, both part of the Upper Proterozoic metasediments of the Bambuí Group of the São Francisco craton. This cratonic cover metamorphosed during the Brazilian Cycle (700-450 million years ago) in a process that resulted in planar structures, such as lineation and foliation, and sub-vertical structures, such as normal and revert faults. The combination of these structures provides the path for the geomorphologic evolution that leads to the rockshelter configurations found in the region. The regional rockshelters and outcrops are developed in the limestone of the Sete Lagoas Formation. More specifically, Lapa do Santo rockshelter developed in the Member Pedro Leopoldo that is composed by very pure limestones with more than 90% calcite. The annual mean temperature is 23 °C, with lower temperatures (11 °C) occurring between June and July and higher temperatures (35 °C) occurring between October and November. The average humidity is around 65% in the dry season, from May to September, and around 85% on the rainy season, from November to April, with a pluviometrical mean of 1,400 mm/year. The major climatic characteristic of this region is the high concentration of rain during the rainy season (93% of total volume). When evaporation is analyzed, the region presents an annual deficit of 176 mm. Despite these particular variations, the regional climate is classified as tropical, with a rainy summer and dry winter. During dry periods, the above ground water sources can become very scarce although underground drainages are capable of keeping the discharge in Velhas River.

The chronology of the site is based on OSL and radiocarbon dating and it defines three distinct human occupation periods with the oldest one starting at 12.7-11.7 cal kyBP (all chronological ranges are based on a 95.4% interval). If we consider a 95.4% confidence interval Lapa do Santo's Period 1 (LSP-1) starts at 12.7 cal kyBP and ends at 7.9 cal kyBP, Lapa do Santo's Period 2 (LSP-2) starts at 5.4 cal kyBP and ends at 3.9 cal kyBP; Lapa do Santo's Period 3 (LSP-3) starts at 2.1 cal kyBP and ends at 0.0 cal kyBP. When the three periods are considered there is a very good agreement between vertical position (i.e., z-value) and dated charcoals showing the stratigraphic integrity of the deposits. At Lapa do Santo a total of 63 charcoal samples were selected for radiocarbon dating. Of those 53 were sent to the Beta Analytic AMS system in Miami and 10 to the Oxford Radiocarbon Accelerator Unit. In total 21 sediment samples were collected for luminescence dating, including two outside the shelter in the lake basin. The samples were mainly collected from test unit Q48 in the northern part of the shelter, from a T-shaped trench extending from the northern to southern part of the shelter, and from test units F13 and M6 in the main area of excavation. Analysis were conducted by Prof. James K. Feathers of the University of Washington. According to the OSL samples the earliest human occupation appears to date from about 9.0 to 12.0 kyBP, consistent with other paleoindian occupations in Lagoa Santa. In the unit F13 dates are at least two thousand years older than the dates obtained from radiocarbon.

Formation process analysis characterizes Lapa do Santo's deposits as mainly anthropogenic and composed by repeated combustion activities, indicating an intense occupation of the same locality over time. The macro stratigraphy of Lapa do Santo shows an intercalation of layers with diffuse to sharp boundaries that can be divided into three main categories, from the more to the less frequent: 1) tabular, grey, centimetric layers of powdery carbonate sediments, with common sand grains and frequent to common red clay aggregates and charcoal (20-40 %); 2) lenticular, red centimetric layers of indurated clay minerals with rare charcoal fragments; 3) lenticular, black, milimetric and centimetric layers, with high concentration of charcoal and microcharcoal. The ash crystals are described as rhombohedric micro-crystalline calcite crystals (10-30 μm). The crystals develop after burning of the calcium oxalates that naturally appear in the plant cells at temperatures around 400-600 °C. Ash crystals, also described as pseudomorphs of calcium oxalate into calcite (POCC), are the diagnostic micromorphological trait of plant ashes. Ash crystals have an overall good preservation. The clay aggregates are always blocky, angular to sub-rounded. They appear in frequencies from 10 to 70% and show three distinct colors: red, orange and yellow. The differences could be related with the natural Fe₂O₃ content or to the anthropic modification of the clay aggregates (by human fires), as suggested by the dark red rims. Bioturbation of the sediments is indicated by channel and chamber voids, seen in most of the thin sections, passage features and large faunal channels. However, bioturbation was generally not intense since fragile components, such as tissue residues, laminations of fine plant tissue and articulated ashes show good integrity. The mixing of geogenic (clay aggregates) and anthropogenic sediments (ashes) seen in Lapa do Santo is a frequent characteristic in rockshelters of Lagoa Santa. Ashes from anthropic fires have been described in the sediments of Lapa das Boleiras and Lapa Grande de Taquaraçu.

Zooarchaeological analysis indicates the presence of fish, lizards, rodents, armadillos, peccaries and deer that were brought as a single piece from the killing site. Results of stable carbon and nitrogen isotopic analysis indicate a diet where protein mainly came from plant food resources. Together with dental caries frequencies comparable to those observed among agricultural populations, the emerging picture is of a typical early Archaic economy structured around staple carbohydrates complemented by hunting of small and mid-sized animals.