Biber's finest scordatura writing is represented in two collections. The first dates from c. 1676 and is known variously as Mystery Sonatas, Rosary Sonatas (Mysterien Sonaten, Die Rosenkranz-Sonaten), Copper-Plate Engraving Sonatas, etc.,[4] remaining unpublished during the composer's lifetime. It comprises sixteen pieces: fifteen sonatas for violin and continuo portraying the fifteen Mysteries of the Rosary, and a long passacaglia for solo violin. In the extant copy of the collection, each piece is accompanied by a small engraving depicting the mystery it portrays, while the image (an ink drawing) preceding the passacaglia depicts a guardian angel with a child. Only the first and the last pieces use normal tuning; all others employ some form of scordatura:

The sonatas were dedicated to Maximilian Gandolph von Khuenburg, whom Biber addresses in the preface: "I have consecrated the whole to the honour of the XV Sacred Mysteries, which you promote so strongly." Although unpublished during the composer's lifetime, these works are his most popular pieces today, and one of the reasons for the revival of interest in his music. The entire set has been recorded by numerous violinists such as John Holloway, Andrew Manze, and many others. Sonata 15 is famous for one of its themes, which matches the theme of Paganini's Caprice No. 24 almost exactly; it is possible that Paganini was inspired by Biber, just as Franz Liszt, Johannes Brahms and Sergei Rachmaninoff were later inspired by Paganini's Caprice.[12]

The second work in which Biber explored scordatura techniques is Harmonia artificioso-ariosa (1696), his last known published collection of instrumental music. It contains seven partitas for two instruments and basso continuo: five for two violins, one for two violas d'amore, and one for violin and viola. Six of the partitas require scordatura tunings, including those for viola and two violas d'amore; Biber utilises the full potential of the technique, including all possibilities for complex polyphony: some of the pieces are in five parts, with both of the melodic instruments carrying two. No other chamber works by Biber use such devices, and the only other pieces to use scordatura are two of the sonatas included in Sonatae violino solo of 1681. That collection comprises eight sonatas for violin and basso continuo, all noted already by Charles Burney in the late 18th century, for the brilliant virtuosic passages and elaborate structures. In contrast to both Mystery Sonatas and Harmonia, these works consist mostly of pieces in free forms (prelude, aria) or variations, rather than dances.

Biber's other published collections of instrumental music are Sonatae tam aris quam aulis servientes (1676), Mensa sonora (1680), and Fidicinium sacro profanum (1682/3). Sonatae tam aris contains sonatas in five, six or eight parts; some of them only use string instruments, some include one or two trumpets. Mensa sonora is a set of six partitas for one or two violins, viola, cello, and basso continuo, and Fidicinium sacro profanum comprises twelve sonatas for one or two violins, two violas, and continuo. Finally, manuscript sources include numerous other pieces: fantasias, balletti, sonatas, etc. Among these are the Battalia, a programmatic "battle" piece which anticipates such latter-day techniques as polytonality and col legno playing,[13] and the Sonata representativa, another typical 17th-century piece similar to works by Walther and Farina, which imitates various birds and animals.[2] An example of Biber's versatility in instrumental music is the Sonata S Polycarpi, which is scored for eight trumpets and timpani.

Unlike most composers for the violin, Biber did not limit himself to music for the instrument. He was also a prolific composer of sacred vocal works: masses, requiems, motets, etc. Many of those were polychoral and employing large instrumental forces, inspired by the possibilities of the spacious interior of the Salzburg Cathedral. Among the polychoral works, Missa Salisburgensis (1682) is the best known. An expansive setting of the mass for sixteen voices and 37 instrumentalists (i.e. 53 parts total), it was previously attributed to Orazio Benevoli, but today Biber's authorship is certain. The instrumentation includes not only string ensembles, but also oboes, cornetts, trumpets, and timpani. Among his many polychoral works are Plaudite tympana à 53 (1682) Vesperae à 32 (1693), Missa Bruxellensis (1696) and Missa Sancti Henrici (1697), which was composed for the occasion of the taking of the veil by his second daughter, Anna Magdalena, at Nonnberg Abbey in Salzburg. In tribute to the Emperor Henry II, the second founding saint of the convent, she took the name Maria Rosa Henrica when her novitiate began in 1696. The Mass of Saint Henry is scored for a five-voice choir with two soprano lines and an orchestra of two violins, three violas, two trumpets, timpani and continuo, with optional extra trumpets and sackbuts to double the voice parts.

Although Biber is best known for the massive polychoral works, he was also capable of writing for smaller forces. Missa quadragesimalis is a simple a cappella setting (with only a continuo part provided) for four voices, as is the Stabat Mater.

• Dann, Elias & Sehnal, Jiří (2001). "Heinrich Ignaz Franz von Biber". In Root, Deane L. (ed.). The New Grove Dictionary of Music and Musicians. Oxford University Press. ‎, Retrieved 25 July 2009