Complex fractionated electrograms (CFAEs) detected during substrate mapping for atrial fibrillation (AF) reflect etiologies that are difficult to separate. Without knowledge of local refractoriness and activation sequence, CFAEs may represent rapid localized activity, disorganized wave collisions, or far-field electrograms. The purpose of this study was to separate CFAE types in human AF, using monophasic action potentials (MAPs) to map local refractoriness in AF and multipolar catheters to map activation sequence. MAP and adjacent activation sequences at 124 biatrial sites were studied in 18 patients prior to AF ablation (age 57 ± 13 years, left atrial diameter 45 ± 8 mm). AF cycle length, bipolar voltage, and spectral dominant frequency were measured to characterize types of CFAE. CFAE were observed at 91 sites, most of which showed discrete MAPs and (1) pansystolic local activity (8%); (2) CFAE after AF acceleration, often with MAP alternans (8%); or (3) nonlocal (far-field) signals (67%). A fourth CFAE pattern lacked discrete MAPs (17%), consistent with spatial disorganization. CFAE with discrete MAPs and pansystolic activation (consistent with rapid localized AF sites) had shorter cycle length (P <.05) and lower voltage (P <.05) and trended to have higher dominant frequency than other CFAE sites. Many CFAEs, particularly at the septa and coronary sinus, represented far-field signals. CFAEs in human AF represent distinct functional types that may be separated using MAPs and activation sequence. In a minority of cases, CFAEs indicate localized rapid AF sites. The majority of CFAEs reflect far-field signals, AF acceleration, or disorganization. These results may help to interpret CFAE during AF substrate mapping.