The global demand for edible bird nests (EBNs) is high, especially from Hong Kong and Peoples Republic of China. Recently, this industry was greatly affected when China banned the import of all the EBNs from Malaysia (except for canned version) due to detection of high levels of nitrites. Several cases of anaphylaxis following ingestion of EBNs were reported. The source(s) of these allergens remain unknown. Mites have been reported to trigger allergic responses. Hence, this study was designed to quantify, isolate and identify the mites that are associated with EBNs. The raw EBNs were purchased from swiftlet farms in five locations in Peninsular Malaysia while the commercial nests were purchased from five different Chinese traditional medicinal shops. The average mite density of all the raw nests was 285 ± 603 mites per gram of EBN while the commercial nests had a much lower mean value of 21 ± 32 mites per gram of EBN (p = 0.082). Among the raw EBNs, the nests from Kajang had the highest average mite density (946 ± 1443 mites/g of EBN) whereas the nests from Kuala Sanglang had the lowest (54 ± 34 mites/g of EBN). Among the commercial EBNs, the nests from Company D had the highest average mite density (76 ± 18 mites/g of EBN) whereas the nests from Company A were free of mites. Overall, the average densities of mites in the raw nests obtained from southern regions of Malaysia (Selangor and Johor) were higher than those nests obtained from the northern regions (Kedah and Kelantan). Thirty types of mites were isolated from both the raw and commercial nests. Among these, some are probably feather mites (Eustathia cultrifer, Pteroherpus garrulacis, Pterodectes amaurochalinus, Laminalloptes sp., Berlesella alata and Neochauliacia sp.), house dust and storage mites (Suidasia sp., Austroglycyphagus sp., and Aleuroglyphus ovatus), mesostigmatid mites (Dermanyssus sp.), prostigmatid mites (Cheyletus sp., tarsonemid and cunaxid mites), astigmatid mites (Collocalidectes sp., Streetacarus sp. and Hemisarcoptes sp.) and oribatid mites. This study provides baseline information on the density and type of mites that are probably associated with EBNs. This study also heightens the importance of mites as a possible source of EBN-associated anaphylaxis.