Baptista recorded with pianist Herbie Hancock on his 2005 release, Possibilities. In 2002 Baptista toured with Yo-Yo Ma’s Brazil Project and also appeared on the Obrigado Brazil album - winner of two Grammy awards. He also toured with Trey Anastasio of Phish and John Zorn. He recorded and performed worldwide with Herbie Hancock’s Grammy award winning Gershwin’s World. Baptista collaborated with Wynton Marsalis and the Lincoln Center Jazz Orchestra for a Brazilian Carnival modern jazz concert. For over two years, he toured with Paul Simon's Rhythm of the Saints tour and appears on his Concert in Central Park release. He also toured worldwide with Sting in 2001.
Baptista has performed or recorded with many artists, including: Trey Anastasio, Laurie Anderson, Derek Bailey, Gato Barbieri, Daniel Barenboim, Kathleen Battle, David Byrne, Dr. John, Brian Eno, Melissa Etheridge, Stephen Kent, Wynton Marsalis, Bobby McFerrin, Medeski Martin & Wood, Robert Palmer, Carlos Santana, Tim Sparks, Spyro Gyra, Sting, James Taylor, Michael Tilson Thomas, Yo-Yo Ma, and John Zorn. He has also played with many noted Brazilian artists such as Badi Assad, Ivan Lins, Marisa Monte, Milton Nascimento, Nana Vasconcelos and Caetano Veloso.
Baptista has performed on five Grammy award winning albums: Yo-Yo Ma’s Obrigado Brazil, Cassandra Wilson’s Blue Light 'Til Dawn, The Chieftains’ Santiago, Ivan Lins’ A Love Affair, and Herbie Hancock’s Gershwin’s World. A documentary on Baptista’s project, Beat the Donkey, recorded for the WGBH-TV Boston program ‘La Plaza’, won 3 New England EMMY Awards in 2002.
Baptista appeared in Nicolas Humbert and Werner Penzel's 1990 documentary film on Fred Frith, Step Across the Border. He has also composed music for programs on the children's television network Nickelodeon.
Baptista formed Beat the Donkey, a percussion and dance ensemble in 2002. The group released its second CD, Love the Donkey on John Zorn's independent Tzadik record label in 2005.
Cyro's debut self-titled CD with Beat the Donkey (Tzadik Records) was picked by John Pareles of The New York Times as one of the ten best alternative albums of 2002. Readers of JAZZIZ and DRUM magazine voted it as “Best Brazilian CD of the Year” and named Cyro "Best Percussionist of 2002." Downbeat Magazine’s 51st annual critics’ poll selected Cyro as ‘Rising Star’ in percussion.
Baptista's first solo recording in 1997, Villa Lobos/Vira Loucos, is a mix of his own compositions with the work of the Brazilian composer Heitor Villa-Lobos. It was called "the most courageous, bright, funny, dramatic, and imaginative work in recent memory."
Blue Note Records released Supergenerous, a duo CD recorded with guitarist Kevin Breit (KD Lang, Cassandra Wilson). Billboard called Supergenerous "pure aural pleasure" and the Washington Post noted it "a marvelous debut that manages to feel outside and intimate at the same time."
Baptista conducts educational "rhythm workshops" in a variety of formats. He has provided presentations for a range of audiences, from elementary school children to professional musicians.
He has conducted workshops and master classes at numerous institutions throughout the world. These include Berklee College of Music (Boston, MA), The New School (New York City), Drummer's Collective (New York City), Mannes College of Music (New York City), New World Symphony Orchestra (Miami, FL) and Rimon School of Music (Tel-Aviv, Israel).