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The method for QSAR modelling of rat acute toxicity based on the combination of QNA (Quantitative Neighbourhoods of Atoms) descriptors, PASS (Prediction of Activity Spectra for Substances) predictions and self-consistent regression (SCR) is presented. PASS predicted biological activity profiles are used as independent input variables for QSAR modelling with SCR. QSAR models were developed using LD50 values for compounds tested on rats with four types of administration (oral, intravenous, intraperitoneal, subcutaneous). The proposed method was evaluated on the set of compounds tested for acute rat toxicity with oral administration (7286 compounds) used for testing the known QSAR methods in T.E.S.T. 3.0 program (U.S. EPA). The several other sets of compounds tested for acute rat toxicity by different routes of administration selected from SYMYX MDL Toxicity Database were used too. The method was compared with the results of prediction of acute rodent toxicity for noncongeneric sets obtained by ACD/Labs Inc. The test sets were predicted with regards to the applicability domain. Comparison of accuracy for QSAR models obtained separately using QNA descriptors, PASS predictions, nearest neighbours' assessment with consensus models clearly demonstrated the benefits of consensus prediction. Free available web-service for prediction of LD50 values of rat acute toxicity was developed: http://www.pharmaexpert.ru/GUSAR/AcuToxPredict/.