The CLIO code solves the Conditional Moment Closure transport equations for reacting scalars. These equations are PDE’s in three space directions, one or two sample space directions (mixture fraction, progress variable, two mixture fractions etc), and time. A fractional step approach is taken for the transport in real space, transport in conserved scalar space, and chemistry. Various stiff solvers have been used such as LIBSC, DVODE, VODEPK, LSODE, CHEMEQ, and various chemical schemes can be implemented. CLIO has been interfaced with various CFD codes in RANS and LES such as openFOAM, PRECISE_uns, FLUENT, and STAR-CD