The microbiological and toxicological quality of 51 samples of dried herbs (Melissa officinalis, Salvia officinalis, Malva sylvestris, Matricaria chamomilla, Alchemilla vulgaris and Centaurea cyanus) cultivated in family-managed farms in Molise Region (Italy) was evaluated.All the samples were analysed by using conventional methods, and for samples preparation, an alternative Washing and Shaking (WaS) protocol was developed to reduce release of antimicrobial compounds. None of the samples were of unsatisfactory quality with respect to aflatoxin B1, and only three samples from Malva sylvestris exceeded the limit of total aflatoxins according to Recommendation 2004/24/EC. The International Commission on Microbiological Specifications for Foods limits for mesophilic bacteria and total coliforms were exceeded in the 29.4 and 3.9% of samples, respectively: 7.8% of samples also exceeded the limit for Escherichia coli established by European Spice Association. When the 'WaS' method was used, higher microbial counts were obtained, especially for A. vulgaris, S. officinalis and M. officinalis.Herbs cultivated in family-managed small agricultural areas showed a good microbiological and toxicological quality, irrespectively of preliminary washing or selection procedures.Herb matrices may contain antimicrobial activity which should be considered when applying the conventional microbiological methods for sample preparation. Alternative preparation protocols may have advantages to reduce antimicrobial effects and should be further evaluated.