Cyro Baptista was born December 23, 1950, in São Paulo, Brazil. In 1980 he moved to the United States on a scholarship to the Creative Music Studio in Woodstock, New York, the free-improvisation-oriented school that placed him inside the same downtown New York orbit as John Zorn, whom he met that decade. Through the 1980s he worked with Zorn on film-scoring projects, and by the 1990s he was a fixture on Zorn's own records as well as albums by fellow Brazilian expatriates Marisa Monte and Milton Nascimento's circle, and by Holly Cole and Cassandra Wilson.

Baptista's first album as a leader, Cyro Baptista Plays the Music of Villa-Lobos: Vira Loucos (1997), came out on Avant, a Japanese avant-garde imprint distributed through the same downtown-New York network as Zorn's own Tzadik label, and reworked Heitor Villa-Lobos's concert music through a percussion-and-improvisation lens rather than presenting original compositions. He followed it by forming Beat the Donkey, a large, carnival-block-party ensemble that made its recorded debut with the self-titled Beat the Donkey (2002, Tzadik), an album crowded with guests: Zorn himself on alto saxophone, Anat Cohen on clarinet and vocals (confined to the track "Parar De Fumar"), guitarists Marc Ribot and Romero Lubambo, cellist Erik Friedlander, bassist Nilson Matta, and vocalist Luciana Souza. A second Beat the Donkey record, Beat the Donkey Beat, followed in 2004.

Later in the 2000s Baptista formed a second band, Cyro Baptista's Banquet of the Spirits, releasing a self-titled debut in 2008 and a second album, Infinito, in 2009 (both Tzadik), the latter again featuring Anat Cohen, this time on clarinet and saxophone. Across the same years and beyond, Baptista became one of the most heavily used percussionists in Zorn's Tzadik universe, appearing on the label's long-running Filmworks soundtrack series, the Masada-family projects Electric Masada and the Bar Kokhba Sextet, the vocal group John Zorn's The Dreamers, and numerous other Zorn productions stretching from the mid-1980s to the 2020s. He also recorded a duo album with British free-improvisation guitarist Derek Bailey, Derek (2006), and released a solo percussion performance film, Solos: The Jazz Sessions (2010). His own catalog continued with Bluefly (2016, Tzadik's Spectrum Series), Chama (2023, Ropeadope), and Triacontagon (2026, Defkaz Records), a trio recording with free-jazz saxophonist Ivo Perelman and guitarist/composer Elliott Sharp.

Running alongside his jazz and avant-garde work has been a long career as an in-demand percussionist for major crossover and pop artists. He toured with Paul Simon for more than two years around 1990-1991, appearing on the live album Paul Simon's Concert in the Park; recorded and toured with Herbie Hancock, including on Hancock's Grammy-winning Gershwin's World (1998) and Possibilities (2005); joined Yo-Yo Ma's Brazil Project, contributing to the two-time Grammy winner Obrigado Brazil (2003); toured worldwide with Sting; and recorded across several Trey Anastasio albums between 2002 and 2021. A credit on the 2013 reissue of Robert Palmer's Heavy Nova documents an earlier connection to that singer as well.

Baptista's honors include being named Best Percussionist by both JAZZIZ and DRUM! magazines in 2002, a Rising Star citation in percussion in DownBeat's 2002 Critics Poll, and a 2009 Fellow Award in Music from United States Artists. He is known for building many of his own instruments and for a stage setup that can include upward of 40 different percussion pieces at once, from berimbau and cuica to instruments of his own invention.

Baptista's playing fuses the folkloric percussion vocabulary of Brazil (candomblé, capoeira, carnival) with the harmonic and structural freedom of downtown New York's avant-garde jazz scene, a combination that made him one of John Zorn's most frequent collaborators across three decades of Tzadik recordings. Where many Brazilian percussionists work inside fixed samba or bossa nova frameworks, Baptista treats his instruments, factory-made and self-built alike, as a full orchestra capable of abrupt shifts between groove, noise, and theater, and his live performances lean into showmanship as much as rhythm. That range let him move fluidly between free-improvisation settings (his duo record with Derek Bailey), electric-Masada-style intensity, and mainstream pop and orchestral sessions for Paul Simon, Yo-Yo Ma, and Herbie Hancock without any of those idioms overwhelming the others.