Display omitted •The optimal parameters in five disinfection processes were determined.•The amounts of total DBPs followed the order of Cl2 > UV/Cl2 > ClO2 > UV ≈ O3.•The amounts of total DBPFP followed the order of UV/Cl2 > UV ≈ Cl2 > O3 > ClO2.•The acute toxicity order of disinfected effluents was Cl2 > UV/Cl2 > ClO2 > UV > O3.•Most of DBPs and DBPFP except TCNMFP were lower in SBTE than those in FPTE. Hospital wastewater (HWW) contains a large number of pathogenic microorganisms; therefore disinfection is an indispensable unit for its treatment. This study compared the formation and formation potential of disinfection by-products (DBPs) and assessed the variations of acute toxicity for both of first physical treatment effluent (FPTE) and second biological treatment effluent (SBTE) of HWW under five different disinfection processes, including free chlorine (Cl2), chlorine dioxide (ClO2), ozone (O3), ultraviolet (UV) and ultraviolet/chlorine (UV/Cl2). Firstly, the optimal parameters of each disinfection process for FPTE and SBTE were determined respectively based on the required disinfection efficiency (i.e., controlling the concentration of fecal coliforms). The amounts of total DBPs in different disinfection processes under the optimal disinfectants dosage followed the order of Cl2 > UV/Cl2 > ClO2 > UV ≈ O3, which demonstrated that the amount of DBPs formation was closely related to the dosage of chlorine. Meanwhile, the amounts of total disinfection by-products formation potential (DBPFP) under the optimal disinfectants dosage followed the order of UV/Cl2 > UV ≈ Cl2 > O3 > ClO2. Besides, it was found that with the reduction of chlorine dosage, the formed DBPs in UV/Cl2 disinfection process decreased. However, UV/Cl2 disinfection process might degrade organic compounds into more DBPs precursors, leading to higher DBPFP than that in Cl2 disinfection process. Significantly, some specific DBPFPs such as haloketones-FP (HKFP), chloral hydrate-FP (CHFP) and trichloronitromethane-FP (TCNMFP) in O3 disinfection process were found higher than that in Cl2 disinfection process, which could be attributed to the formation of O3 oxidation by-products, for instance aldehydes, methyl ketones and trivalent nitrogen compounds. Additionally, apart from O3, the growth inhibition rate of Chlorella vulgaris increased in all the other disinfection processes and the order of the acute toxicity in each disinfected effluent was consistent with that of DBPs formation.