A total of 102 honey samples collected from small apiaries (≤ 20 hives) in Poland were analysed for the presence of Clostridium botulinum spores. The samples were prepared using the dilution centrifugation method and cultured in parallel in cooked meat medium (CMM) and tripticase peptone glucose yeast (TPGY) enrichment broths. Identification of toxin types A, B, and E of Clostridium botulinum strains was performed with the use of the multiplex PCR method. Positive samples were also subjected to quantitative analysis with the use of Clostridium botulinum Isolation Agar Base (CBAB). The prevalence analysis showed 22 (21.6%) samples contaminated with C. botulinum spores. The major serotype detected was botulin neurotoxin type A – 16 (72.7%) whereas type B was found in 3 (13.6%) honey samples and type E also only in 3 (13.6%) honey samples. Dual-toxin-producing strains were noted. The average quantity of spores in PCR - C. botulinum positive samples was 190 in 1 gram of honey.