The effects of feeding autoclaved commercial SSNIFF (SN) diet and diets containing soya bean (S) and casein (C) to growing conventional (CON) and specified pathogen-free (SPF) rats were determined. Diets S, C and SN, autoclaved at 121 °C during 20 min (T1), at 134 °C during 10 min (T2) and non-autoclaved (T0), were fed during four weeks, each to 8 CON males and 8 females of mean initial body weight 56 g, kept individually. Diets S, C and SN, autoclaved at T1, were fed during two months, each to 20 SPF males and 20 females of mean initial body weight 58 g, kept in group of 5 animals per cage. In CON rats, autoclaving did not affect feed intake and weight gain, decreased thyroid and stomach weight, increased caecal tissue and digesta weight, and concentrations of isobutyric, isovaleric and valeric acid in caecal digesta. Among biochemical blood parameters, autoclaving decreased only total protein concentration and aspartate aminotransferase activity. Feeding C diet resulted in lower feed intake and weight gain in CON and SPF males. Diet affected organ weights and the greatest differences were found in rats on SN diet for weights of stomach, caecum and female reproductive organs. Diet affected concentration of all short-chain fatty acids, pH and weight of caecal digesta, the most important being the greatest butyric acid concentration on SN diet and isoacids on C diet. It is concluded that autoclaving of both soya-containing and soya-free diets does not affect negatively animal performance and physiology.