Pre-Columbian rafts plied the Pacific Coast of South America for trade from about 100 BCE, and possibly much earlier. The 16th-century descriptions by the Spanish of the rafts used by Native Americans along the seacoasts of Peru and Ecuador has incited speculation about the seamanship of the Indigenous, the seaworthiness of their rafts, and the possibility that they undertook long ocean-going voyages. None of the prehistoric rafts have survived and the exact characteristics of their construction and the geographical extent of their voyages are uncertain.

It is likely that traders using rafts, constructed of balsa wood logs, voyaged as far as Mexico and introduced metallurgy to the civilizations of that country. Some scholars and adventurers of the 20th and 21st century (most notably Thor Heyerdahl) who reached Polynesia on the Kon-Tiki raft have asserted that the rafts and their crews journeyed thousands of miles across the Pacific to Polynesia. Several other people and groups have also built rafts based on prehistoric models and undertaken trans-Pacific voyages.

Balsa is the Spanish word for raft. The use of rafts for commerce on the coasts of Peru and Ecuador, from northern Chile to southern Colombia, continued until the late 19th century, long after the Spanish conquest of the Inca Empire (1532 to 1572), although the fidelity of these rafts to their prehistoric ancestors is uncertain.

In 1526, a Spanish ship captained by Bartolomé Ruiz, Francisco Pizarro's chief navigator, ventured southward down the west coast of South America, the first Old World ship known to have explored this coastline. Off the coast of Ecuador, Ruiz encountered a Native American raft, being the first encounter between the Spanish and the Inca's vassals. A contemporary account of the encounter is:

[The Spanish] captured a ship [raft] with as many as 20 men aboard of whom 11 threw themselves into the water. [Ruiz] put the remainder of the crew onshore except for three whom he kept as interpreters. He treated them well. The ship he took had a capacity of up to 30 toneles [25 metric tons]. The keel was made of canes [balsa logs] as thick as posts bound together with ropes of what they call henequen, which is like hemp. It had an upper deck made of lighter canes, tied with the same kind of ropes. The people and their cargo remained dry on the upper deck, as the lower logs were awash in the seawater. The ship had masts of good wood and lateen-rigged sails of cotton, the same as our ships, and good rigging with henequen ropes. It carried stone weights like barber's grinding stones as anchors.

The chronicler, Francisco de Xerez, said that the raft carried a cargo of "silver objects, tiaras, crowns, bands, tweezers and bells, all of this they brought to exchange for some [sea] shells." Other contemporary chroniclers gave additional details about the rafts. "They set a mast in the largest log in the middle, hoist and sail, and navigate all along this coast. They are very safe vessels because they cannot sink or capsize, since the water washes through them."

Logs from the balsa tree (Ochroma lagopus) are distinguished by their light weight and large size (up to 90 centimetres (35 in) in diameter). A tree of the tropical forest, the balsa tree did not naturally occur on the arid coasts of Peru and southern Ecuador. The source of balsa logs for rafts was the valley of the Guayas River, north of the city of Guayaquil, Ecuador. This area is still the principal source of balsa wood for international trade.

The long-term buoyancy of balsa logs has been called into question. Prior to the voyage across the Pacific Ocean of the Kon-Tiki in 1947, scholars often argued that balsa logs absorb water so quickly that long voyages were infeasible. Heyerdahl, however, used green balsa wood logs for a voyage of 101 days on the Kon-Tiki. Other studies have also indicated that dry balsa logs can remain afloat for extended periods of time.