Fernando Boteros Werke sind in folgenden Museen und Sammlungen vertreten (Auszug):
 |
 | Hiroshima City Museum of Contemporary Art, Japan |
| Hirshhorn Museum and Sculpture Garden, Smithsonian Institution, Washington, D.C. |
| Ho-am Museum, Seoul, Süd Korea |
| Hood Museum of Art, Dartmouth College, Hanover, New Hampshire |
| Israel Museum, Jerusalem |
| Kunsthalle Nürnberg, Deutschland |
| Lowe Art Museum, University of Miami, Coral Gables, Florida |
| University, Rochester, Michigan |
| The Metropolitan Museum of Art , New York |
| Milwaukee Art Museum, Wisconsin |
| Miyagi Museum of Art, Japan |
| Museo d´Arte Moderna del Vaticano, Rom, Italien |
| Museo de Antioquia, Medellín, Kolumbien |
| Museo de Arte Contemporaneo de Caracas, Venezuela |
| Museo de Arte Moderno, Bogotá, Kolumbien |
| Museo de Bellas Artes, Caracas, Venezuela |
| Museo Nacional, Bogotá, Kolumbien |
| Museo Nacional de Bellas Artes, Santiago, Chile |
| Museum Moderne Kunst, Vienna, Österreich |
| The Museum of Modern Art, New York |
| The Museum of Modern Art, Saitama, Japan |
| Neue Pinakothek, München, Deutschland |
| Ponce Museum of Art, Ponce, Puerto Rico |
| Pushkin Museum, Moscow, Russland |
| The Solomon R. Guggenheim Museum, New York |
| Staatsgalerie Moderne Kunst, München, Deutschland |
| The State Hermitage Museum, St. Petersburg, Russland |
| Tokushima Modern Art Museum, Japan |
| Wallraf-Richartz-Museum, Köln, Deutschland |
| Yamanashi Prefectural Museum of Art, Japan |