Aims: To clarify the usefulness of preservative-free ophthalmic preparations equipped with a filter. Methods: A total of 1,615 samples of in-use ophthalmic preparations were examined for microbial contamination. Results: Of 1,094 samples of preservative-containing ophthalmic preparations, 31 (2.8%) showed microbial contamination. Of 289 samples of preservative-free ophthalmic preparations without a filter, 6 (2.1%) were contaminated, consisting of 4 (13.8%) of 29 samples of hospital preparations and 2 (0.8%) of 260 samples of commercially available new quinolone antimicrobial agents. On the other hand, the microbial contamination rate in preservative-free ophthalmic preparations equipped with a filter was 0% (0 of 232 samples).The major contaminants detected in these preservative-containing ophthalmic preparations and preservative-free ophthalmic preparations without a filter were glucose-nonfermentative Gram-negative bacilli such as Pseudomonas fluorescens, Acinetobacter spp., and P. aeruginosa, coagulase (-) staphylococci, and Candida spp. The contaminant level was 10-99 colony forming units (CFU)/mL in 37.8% (14 of 37 samples), and 10^2 - 10^6 CFU/mL in 62.2% (23 of 37 samples). Conclusions: Preservative-free ophthalmic preparations equipped with a filter not only have zero risk of the oculotoxic effects of preservatives, but are also safe in terms of their lack of microbial contamination.