The counts of different groups of organisms (mesophilic total aerobic and anaerobic bacteria, enterobacteriaceae, faecal coliform bacteria and faecal streptococci type D), as well as the presence or absence of Pseudomonas spp. and Salmonella spp., were recorded in both unfiltered and filtered pig slurry samples at 1, 8 and 29 days of storage, before and after applying N-duopropenide (a new disinfectant with a quaternary ammonium structure) at 1, 2 x 1, 5 and 2 x 5% concentrations of the commercial product (equivalent to 0.11, 2 x 0.11, 0.55 and 2 x 0.55%, respectively, of active ingredient) for 1 h, or 0.5% commercial formaldehyde for 6 days. Before disinfection, anaerobic and aerobic organisms resulted in the highest counts (between 6 and 7 log units/ml), followed by enterobacteriaceae, faecal coliforms and streptococci (4-5 log units/ml). The unfiltered slurry showed higher bacterial counts than the filtered slurry. The variation in counts was similar for all the groups studied, with the highest count on day 1 of storage with a continuous decrease over the 3 days studied. N-duopropenide efficacy depended on the dose used, but a 2 x 5% concentration resulted in total inactivation (100% reduction) of all the bacteria studied, except for the total aerobic and anaerobic organisms present in unfiltered slurry. Formaldehyde efficacy was much lower. In respect of Pseudomonas spp., more isolates were obtained after using N-duopropenide at lower concentrations (1 and 2 x 1%) than before treatment, thus suggesting its suitability for selective isolation of this genus. Finally, no Salmonella spp. strains were isolated in any of the cases considered in this study.