In a first embodiment, this invention includes an integrated robot apparatus for performing combinatorial chemistry synthesis protocols and having interchangeable work-stations, robot arm tools, and reaction vessels and reaction vessel arrays. The work-stations and tools are specialized to perform tasks necessary for the synthesis in a plurality of the reaction vessels grouped in a plurality of the reaction vessel arrays. Preferably, these elements function interchangeably because they have standardized sizes and conformation. The work-stations and tools include those for fluid dispensing or aspirating from individual reaction vessels or from all the reaction vessels in an array simultaneously. The reaction vessels can include, alternatively, stackable, ball-sealed reaction vessels, microtitre-like reaction vessel arrays, arrays of independent reaction vessels, valve-sealed reaction vessels, septum-sealed reaction vessels, and syringe reaction vessels. In alternative embodiments, this invention includes these work-stations, tools, reaction vessels and reaction vessel arrays in various combinations or sub-combinations either for use in partially integrated robots or for manual or standalone use.