A distinction has been made by some modern researchers between the smaller bead-sized crystal skulls, which first appear in the mid-19th century, and the larger (approximately life-sized) skulls that appear toward the end of that century. The larger crystal skulls have attracted nearly all the popular attention in recent times, and researchers believe that all of these have been manufactured as forgeries in Europe.

Trade in fake pre-Columbian artifacts developed during the late 19th century to the extent that in 1886 Smithsonian archaeologist William Henry Holmes wrote an article called "'The Trade in Spurious Mexican Antiquities"' for Science. Although museums acquired skulls earlier, it was Eugène Boban, an antiquities dealer who opened his shop in Paris in 1870, who is most associated with 19th-century museum collections of crystal skulls. Most of Boban's collection, including three crystal skulls, was sold to the ethnographer Alphonse Pinart, who donated the collection to the Trocadéro Museum, which later became the Musée de l'Homme.

Many crystal skulls are claimed to be pre-Columbian, usually attributed to the Aztec or Maya civilizations. Mesoamerican art has numerous representations of skulls, but none of the skulls in museum collections come from documented excavations. Research carried out on several crystal skulls at the British Museum in 1967, 1996 and again in 2004 has shown that the indented lines marking the teeth (for these skulls had no separate jawbone, unlike the Mitchell-Hedges skull) were carved using jeweler's equipment (rotary tools) developed in the 19th century, making a supposed pre-Columbian origin problematic. The type of crystal was determined by examination of chlorite inclusions, and is only to be found in Madagascar and Brazil, and thus unobtainable or unknown within pre-Columbian Mesoamerica. The study concluded that the skulls were crafted in the 19th century in Germany, quite likely at workshops in the town of Idar-Oberstein renowned for crafting objects made from imported Brazilian quartz at this period in the late 19th century.

It has been established that both the British Museum and Paris's Musée de l'Homme crystal skulls were originally sold by the French antiquities dealer Eugène Boban, who was operating in Mexico City between 1860 and 1880. The British Museum crystal skull transited through New York's Tiffany's, whilst the Musée de l'Homme's crystal skull was donated by Alphonse Pinart, an ethnographer who had bought it from Boban.

An investigation carried out by the Smithsonian Institution in 1992 on a crystal skull provided by an anonymous source who claimed to have purchased it in Mexico City in 1960 and that it was of Aztec origin concluded that it, too, was made in recent years. According to the Smithsonian, Boban acquired the crystal skulls he sold from sources in Germany – findings that are in keeping with those of the British Museum.

A detailed study of the British Museum and Smithsonian crystal skulls was accepted for publication by the Journal of Archaeological Science in May 2008. ] Using electron microscopy and X-ray crystallography, a team of British and American researchers found that the British Museum skull was worked with a harsh abrasive substance such as corundum or diamond, and shaped using a rotary disc tool made from some suitable metal. The Smithsonian specimen had been worked with a different abrasive, namely the silicon-carbon compound carborundum which is a synthetic substance manufactured using modern industrial techniques. Since the synthesis of carborundum dates only to the 1890s and its wider availability to the 20th century, the researchers concluded "[t]he suggestion is that it was made in the 1950s or later".

Individual skulls

Perhaps the most famous and enigmatic skull was allegedly discovered in 1924 by Anna Le Guillon Mitchell-Hedges, adopted daughter of British adventurer and popularist author F.A. Mitchell-Hedges. It is the subject of a video documentary made in 1990, Crystal Skull of Labaantun. It has been noted upon examination by Smithsonian researchers to be "very nearly a replica of the British Museum skull--almost exactly the same shape, but with more detailed modeling of the eyes and the teeth."

Anna Hedges claimed that she found the skull buried under a collapsed altar inside a temple in Lubaantun, in British Honduras, now Belize. As far as can be ascertained, F.A. Mitchell-Hedges himself made no mention of the alleged discovery in any of his writings on Lubaantun. Also, others present at the time of the excavation have not been documented as noting either the skull's discovery or Anna's presence at the dig.

In a 1970 letter, Anna also stated that she was "told by the few remaining Maya, that the skull was used by the high priest to will death". The artifact is sometimes referred to as "The Skull of Doom" as Mitchell-Hedges claimed it could be used to will death (see below). An alternative explanation is a play on 'Skull of Dunn' (Dunn being an associate of Mitchell-Hedges) . Anna Mitchell-Hedges toured with the skull from 1967 exhibiting it on a pay-per-view basis, and she continued to give interviews about the artifact until her death in 2007.

The skull is made from a block of clear quartz about the size of a small human cranium, measuring some 5 inches (13 cm) high, 7 inches (18 cm) long and 5 inches wide. The lower jaw is detached. In the early 1970s it came under the temporary care of freelance art restorer Frank Dorland, who claimed upon inspecting it that it had been "carved" with total disregard to the natural crystal axes without the use of metal tools. Dorland reported being unable to find any tell-tale scratch marks, except for traces of mechanical grinding on the teeth, and he speculated that it was first chiseled into rough form, probably using diamonds, and the finer shaping, grinding and polishing was achieved through the use of sand over a period of 150 to 300 years. He said it could be up to 12,000 years old. Although various claims have been made over the years regarding the skull's physical properties, such as an allegedly constant temperature of 70°F (21°C), Dorland reported that there was no difference in properties between it and other natural quartz crystals.

While in Dorland's care the skull came to the attention of writer Richard Garvin, at the time working at an advertising agency where he supervised Hewlett-Packard's advertising account. Garvin made arrangements for the skull to be examined at HP's crystal labs at Santa Clara, where it was subjected to several tests. The labs determined only that it was not a composite (as Dorland had supposed), but that it was fashioned from a single crystal of quartz. The lab test also established that the lower jaw had been fashioned from the same left-handed growing crystal as the rest of the skull. No investigation was made by HP as to its method of manufacture or dating.

As well as the traces of mechanical grinding on the teeth noted by Dorland, Mayanist archaeologist Norman Hammond reported that the holes (presumed to be intended for support pegs) showed signs of being made by drilling with metal. Anna Mitchell-Hedges refused subsequent requests to submit the skull for further scientific testing.

F. A. Mitchell-Hedges mentioned the skull only briefly in the first edition of his autobiography, Danger My Ally (1954), without specifying where or by whom it was found. He merely claimed that "it is at least 3,600 years old and according to legend it was used by the High Priest of the Maya when he was performing esoteric rites. It is said that when he willed death with the help of the skull, death invariably followed". All subsequent editions of Danger My Ally omitted mention of the skull entirely.

The earliest published reference to the skull is the July 1936 issue of the British anthropological journal Man, where it is described as being in the possession of Mr. Sydney Burney, a London art dealer who is said to have owned it since 1933. No mention was made of Mitchell-Hedges. There is documentary evidence that Mitchell-Hedges bought it from Burney in 1944. The skull was in the custody of Anna Mitchell-Hedges, the adopted daughter of Frederick. She steadfastly refused to let it be examined by experts (making very doubtful the claim that it was reported on by R. Stansmore Nutting in 1962). Somewhere between 1988–1990 Anna Mitchell-Hedges toured with the skull.

In her last eight years, Anna Mitchell-Hedges lived in Chesterton, Indiana, with Bill Homann, whom she married in 2002. She died on April 11, 2007. Since that time the Mitchell-Hedges Skull has been in the custody of Bill Homann. In April 2009, Five, a television channel, took the story and revealed that the Mitchell-Hedges Skull, recently tested under a special microscope in the Smithsonian Institution, had been manufactured with tools that Aztecs and Mayans simply did not have. Like the other skulls, this one is a fabrication dating from the second half of the 19th century. Bill Homann however continues to believe in its mystical properties.

The crystal skull of the British Museum first appeared in 1881, in the shop of the Paris antiquarian, Eugène Boban. Its origin was not stated in his catalog of the time. He is said to have tried to sell it to Mexico's national museum as an Aztec artifact, but was unsuccessful. Boban later moved his business to New York City, where the skull was sold to George H. Sisson. It was exhibited at the meeting of the American Association for the Advancement of Science in New York City in 1887 by George F. Kunz. It was sold at auction, and bought by Tiffany and Co., who later sold it at cost to the British Museum in 1897. This skull is very similar to the Mitchell-Hedges skull, although it is less detailed and does not have a movable lower jaw.

The British Museum catalogs the skull's provenance as "probably European, 19th century AD" and describes it as "not an authentic pre-Columbian artefact". It has been established that this skull was made with modern tools, and that it is not authentic.

The largest of the three skulls sold by Eugène Boban to Alphonse Pinart (sometimes called the Paris Skull), about 10 cm (4 in) high, has a hole drilled vertically through its center. It is part of a collection held at the Musée du Quai Branly, and was subjected to scientific tests carried out in 2007–08 by France's national Centre de recherche et de restauration des musées de France (Centre for Research and Restoration of the Museums in France, or C2RMF). After a series of analyses carried out over three months, C2RMF engineers concluded that it was "certainly not pre-Columbian, it shows traces of polishing and abrasion by modern tools." Particle accelerator tests also revealed occluded traces of water that were dated to the 19th century, and the Quai Branly released a statement that the tests "seem to indicate that it was made late in the 19th century."

In 2009 the C2RMF researchers published results of further investigations to establish when the Paris skull had been carved. Scanning electron microscopy (SEM) analysis indicated the use of lapidary machine tools in its carving. The results of a new dating technique known as quartz hydration dating (QHD) demonstrated that the Paris skull had been carved later than a reference quartz specimen artefact, known to have been cut in 1740. The researchers conclude that the SEM and QHD results combined with the skull's known provenance indicate it was carved in the 18th or 19th century.

Claims of the healing and supernatural powers of crystal skulls have no support in the scientific community, which has found no evidence of any unusual phenomena associated with the skulls nor any reason for further investigation, other than the confirmation of their provenance and method of manufacture.

Another novel and historically unfounded speculation ties in the legend of the crystal skulls with the completion of the current Maya calendar b'ak'tun-cycle on December 21, 2012, claiming the re-uniting of the thirteen mystical skulls will forestall a catastrophe allegedly predicted or implied by the ending of this calendar. An airing of this claim appeared (among an assortment of others made) in The Mystery of the Crystal Skulls, a 2008 program produced for the Sci Fi Channel in May and shown on Discovery Channel Canada in June. Interviewees included Richard Hoagland, who attempted to link the skulls and the Maya to life on Mars, and David Hatcher Childress, proponent of lost Atlantean civilizations and anti-gravity claims.

Crystal skulls are also referenced by author Drunvalo Melchizedek in his book Serpent of Light. He writes that he came across indigenous Mayan descendants in possession of crystal skulls at ceremonies at temples in the Yucatan, which he writes contained souls of ancient Mayans who had entered the skulls to await the time when their ancient knowledge would once again be required. The book is a log of the authors experiences, which are related in a manner requiring suspension of judgment.

The alleged associations and origins of crystal skull mythology in Native American spiritual lore, as advanced by neoshamanic writers such as Jamie Sams, are similarly discounted.[53] Instead, as Philip Jenkins notes, crystal skull mythology may be traced back to the "baroque legends" initially spread by F.A. Mitchell-Hedges, and then afterwards taken up:

By the 1970s, the crystal skulls [had] entered New Age mythology as potent relics of ancient Atlantis, and they even acquired a canonical number: there were exactly thirteen skulls.
None of this would have anything to do with North American Indian matters, if the skulls had not attracted the attention of some of the most active New Age writers.