High Efficiency Clean Combustion (HECC) strategies such as homogenous charge compression ignition (HCCI) and pre-mixed charge compression ignition (PCCI) offer much promise for the reduction of NOx and PM from diesel engines. While delivering low PM and low NOx, these combustion modes often produce much higher levels of CO and HC than conventional diesel combustion modes. In addition, partially oxygenated species such as formaldehyde (an MSAT) and other aldehydes increase with HECC modes. The higher levels of CO and HCs have the potential to compromise the performance of the catalytic aftertreatment, specifically at low load operating points. As HECC strategies become incorporated into vehicle calibrations, manufacturers need to avoid producing MSATs in higher quantities than found in conventional combustion modes. This paper describes research on two different HECC strategies, HCCI and PCCI. Engine-out data for several MSAT species (formaldehyde, acetaldehyde, benzene, toluene, ethylbenzene, xylenes, naphthalene, PAHs, diesel PM) as well as other HC species are presented and compared when possible with conventional operation. In addition, catalyst-out values were measured to assess the destruction of individual MSATs over the catalyst. At low engine loads, MSATs were higher and catalyst performance was poorer. Particle sizing results identify large differences between PM from conventional and HECC operation.