Objectives To investigate pre- and post-total middle ear reconstruction bacteriological changes in order to facilitate prevention and treatment of surgical infections. Methods Specimens from 128 ears in 124 patients with problematic mastoid cavities who underwent revision total middle ear reconstruction were studied. Results Bacteriological tests were positive in 87(68.0%) pre-operative specimens, despite local treatment, and in 74 (57.8%) specimens collected 10 days after operation. Common organism strains in pre- and post-operative specimens were slightly different and included: coagulase- staphylococcus, GRAM+ rods, staphylococcus aureus, pseudomonas aeruginosa and fungi. At the time of patient discharge (15-20 days post-operative), only 3 ears (2.3%) were tested positive which responded well to and became dry after local treatment. At one year, 4 ears (3.1%) showed recurrent otorrhea which again responded to local treatment. Conclusion For infection of problematic mastoid cavities after an open cavity procedure, revision total middle ear reconstruction is effective in controlling infection and promoting a dry ear. Infection prevention and treatment is important considering the relatively high rates of peri-operative local infections.