Indigo is a universal organic chemistry toolkit. It contains tools for end users, as well as a documented API for developers. It is based on a cheminformatics library that incorporates a number of unique algorithms developed by GGA Software Services, as well as some standard algorithms well known in the cheminformatics world. The API allows developers to integrate Indigo into their C/Java/C#/Python projects. Two Indigo-based Java GUI applications are provided: Legio (combinatorial chemistry) and chemdiff (visual comparison of two SDF or SMILES files). Three Indigo-based command line utilities written in plain C are provided: indigo-depict (molecule and reaction rendering utility), indigo-cano (canonical SMILES generator), and indigo-deco (R-Group deconvolution utility).