Pathogens occurring in particulate foods may be unevenly distributed, which may impact interpretation of most-probable-number (MPN) values. The MPN analysis of Salmonella in naturally contaminated raw almonds was conducted using two sample preparation methods. Raw almond kernels (3,698 samples) and inshell almonds (455 samples) were collected from almond processors throughout California during the 2006 and 2007 harvests, and 100-g samples were enriched for Salmonella. The prevalence of Salmonella on kernels and inshell almonds was 1.6 and 0.9%, respectively, in 2006, and 0.83 and 2.2%, respectively, in 2007. Almond kernel samples from 2006 were further enriched for Salmonella, and levels of the organism were determined for positive samples by three-tube MPN analysis (25 g, 2.5 g, 0.25 g). Almonds were either divided into subsamples prior to blending and enrichment (method A), or samples were blended in enrichment broth prior to preparation of subsamples (method B). Salmonella was not isolated (<1.2 MPN/100 g) upon retesting of 19 of 31 (method A) or 23 of 29 (method B) positive samples. When detected, levels were 1.4 to 15.5 MPN/100 g (average 2.3 MPN/100 g) or 1.4 to 18.3 MPN/100 g (average 2.1 MPN/100 g) using methods A or B, respectively. A total of 23 different Salmonella serovars were identified from the original almond samples. Salmonella Muenchen was the most frequently isolated serovar (15%) from the 53 Salmonella-positive samples, followed by Newport (12%), Enteritidis (10%), and Typhimurium (8%). No correlation was found between presence of Salmonella and E. coli levels, aerobic plate counts, or counts of yeasts or molds.