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Simple Summary: Soy is the major source of protein in animal feeds worldwide. In Europe, only GMO-free varieties may be cultivated. Their chemical composition, contamination by fungi and yeast and the acceptable level in the diet of pigs have not been fully determined yet. This work comprised extensive analyses, both chemical (the composition of amino acids and anti-nutritional factors) and microbiological, also including mycotoxins. Moreover, digestibility and performance parameters were studied in 48 male post-weaning piglets for 28 days using diets, in which soybean meal was replaced by 0%, 5%, 10%, 15%, 20% and 25% soybean seed addition. The chemical composition of soybean seeds differed in terms of crude protein, ether extract, neutral detergent fibre and antinutrient contents. Seeds were also contaminated (but to varying intensity, which may have been influenced by the weather conditions during the seed harvest period) with fungi, yeast and mycotoxins, mainly zearalenone and deoxynivalenol. The digestibility coefficients of crude protein and dry matter in the diet were similar. Pigs' performance parameters were reduced strongly with increasing amounts of raw seeds in their diets, so a 5% of raw soy seed supplementation in pigs' diet is recommended. The aim of this study was to compare the chemical composition of European soy seeds. A mycological and toxigenic screening was carried out on 18 varieties of soy seeds harvested in Poland. Moreover, the level of soybean meal (SBM) substitution by raw soybean seeds was analysed in terms of its effect on young pigs' performance (body weight gain, feed intake, feed utilisation) along with apparent total tract digestibility (ATTD) of dry matter and crude protein in the diets. In a 28-day trial, 48 male pigs were tested using a marker method with TiO2. In their diets, SBM was replaced by soy seeds in the amounts of 0%, 5%, 10%, 15%, 20% and 25%. In the last 3 days of the experiment, samples of excreta from each animal separately were collected three times per day. The chemical composition of soybean seeds differed in terms of their contents of crude protein, ether extract, neutral detergent fibre and raffinose family oligosaccharides, as well as the trypsin inhibitor activity. Seeds were also contaminated with fungi, yeast and mycotoxins, mainly zearalenone and deoxynivalenol. The ATTD of crude protein ranged from 70.6% to 77.6% and that of dry matter from 93.5% to 94.6%, with no differences between the groups being found (p > 0.05). Pigs' performance parameters were reduced strongly with increasing amounts of raw seeds in the diets (p < 0.05). The results indicate that only a 5% addition of raw soy seeds in pigs' diet is recommended. [ABSTRACT FROM AUTHOR]