Polymerase chain reaction (PCR)-based identification of Bacillus thuringiensis toxin genes has become a routine step in most B. thuringiensis isolation and characterization initiatives. In the present study we propose a simplified method for extensive PCR analysis of B. thuringiensis cry and cyt genes of particular interest in large-scale screening programs. Fifty B. thuringiensis strains were screened for the presence of genes of the cry1 subfamily. Identical results were obtained when our method was used in comparison to other methodology based on a standard alkaline lysis preparation of plasmid DNA. Additional tests evidenced the fitness of our method in a particular multiplex–PCR analysis. The main advantages of the proposed methodology are that it is simpler and quicker than commonly used protocols (as DNA template preparation is substituted by direct addition of small amounts of B. thuringiensis liquid cell suspension to the reaction mixture) and that it allows simultaneous handling (bacterial growth and PCR) of up to 96 strains per round.