In this study, the effects of various processing steps applied during apple juice processing on Alicyclobacillus acidoterrestris were investigated. Raw apple juice was inoculated with A. acidoterrestris spores at two inoculum levels of 1 x 10(3) cfu/ml and 1 x 10(6) cfu/ml. Following enzymatic treatment, the raw juice was processed into clear juice using either conventional clarification or ultrafiltration. The number of A. acidoterrestris spores in the final product was determined to be dependent on both initial contamination level and processing conditions. Increasing temperature to 50degreesC during depectinization resulted in a higher spore counts at both inoculum levels. Even if the ultrafiltration process was found to be much more convenient for the retention of A. acidoterrestris when compared to conventional clarification. the spores could penetrate the ultrafiltration membranes having both 20 and 50 kDa. Increasing membrane pore size and initial spore counts in the feed solution also increased the number of spores penetrating the membrane during ultrafiltration.