The occurrence and reactivation of viable but non-culturable (VBNC) Escherichia coli after different anaerobic digestions and the subsequent dewatering and storage were evaluated and compared. Culturable E. coli in digested sludge increased by two to four orders of magnitudes immediately after dewatering. However, counts of both the total and viable E. coli indicated that the increase of E. coli was attributed to its reactivation from the VBNC state to the culturable state. The VBNC pathogen incidences of thermophilic digestion were two to three orders of magnitude higher than those of mesophilic digestion. Accordingly, culturable E. coli in thermophilic, digested sludge after storage were one order of magnitude higher than mesophilic digestion. Anaerobic digestion thus mainly alters the culturable state of pathogens rather than killing them; therefore the biological safety of digested sludge, especially temperature-phased anaerobic digestion, should be carefully assessed.