Salmonella spp. are one of the most common causes of bacterial food-borne diseases worldwide (34). In the United States nontyphoidal Salmonella serotypes cause an estimated 1.4 million human salmonellosis cases, including approximately 550 deaths annually (27). Serotyping with the Kaufmann-White scheme is used commonly as a first step to differentiate Salmonella isolates. Serotyping of Salmonella isolates is based on lipopolysaccharide moieties on the cell surface (O antigens) and the flagellar proteins (H antigens), as well as capsular protein antigens (Vi antigen), which are only found in a few Salmonella serotypes (e.g., Salmonella enterica serotype Typhi). According to the Kaufmann-White scheme, Salmonella includes over 2,500 recognized serotypes (20). Many Salmonella bacteria are motile due to peritrichous flagella (28), which include a basal body, a propeller, and a hook. The motility of Salmonella depends on the rotation of the flagellar propeller (i.e., the filament), which includes either FliC (phase 1 antigen) or FljB (phase 2 antigen) flagellin (11). Most Salmonella serotypes, including Salmonella enterica serotype Typhimurium, are biphasic, meaning that they can express two distinct flagellar antigens (i.e., phase 1 and phase 2 antigens). Regulation of phase 1 and 2 antigen expression is under the control of the recombinase Hin. This recombinase facilitates inversion of a promoter element so that it either (i) transcribes fljB (which encodes the phase 2 antigen FljB) and fljA (which encodes a repressor of fliC, the gene encoding the phase 1 antigen FliC) (4, 37) or (ii) does not transcribe either of these genes. If this promoter is located in an orientation that does not allow for transcription of fljB and fljA, the lack of a repression of fliC transcription leads to expression of phase 1 flagellar antigens. Salmonella enterica serotype 4,5,12:i:− is a serotype that appears to be antigenically similar and genetically closely related to Salmonella serotype Typhimurium (which has the antigenic formula 4,5,12:i:1,2) but lacks expression of the second-phase flagellar antigen, which is 1,2 in Salmonella serotype Typhimurium (28). Salmonella serotype 4,5,12:i:− was the sixth most common Salmonella serotype among cases of human disease in the United States in 2006 (10) and the fourth most common serotype among human isolates in Spain in 1998 (18). Overall, the prevalence of Salmonella serotype 4,5,12:i:− among human cases has increased considerably in many countries in the world over the last 10 years (9, 10, 18, 29, 36). This Salmonella serotype has also been responsible for a number of human salmonellosis outbreaks over the last decades, including in Spain (1998), the United States (2004 and 2007), and Luxemburg (2006). Salmonella serotype 4,5,12:i:− has been isolated, particularly over the last decade, from a number of different foods and animals (1, 6, 13, 29, 38). While a number of separate studies, using molecular subtyping and characterization tools (e.g., genomic microarrays and PCR assays to test for gene presence/absence), have shown that Salmonella serotype 4,5,12:i:− isolates from Spain (15, 18) and the United States (1, 2, 38) are genetically closely related to Salmonella serotype Typhimurium, we are not aware of any comparative studies of Salmonella serotype 4,5,12:i:− isolates from Europe and the United States that have been published to date. In order to provide a better understanding of the transmission, ecology, and evolution of Salmonella serotype 4,5,12:i:−, we have assembled a collection of 190 Salmonella serotype 4,5,12:i:− and Typhimurium isolates from various sources and from two countries, the United States and Spain. These isolates were characterized by different molecular subtyping methods (i.e., multilocus sequence typing [MLST] and pulsed-field gel electrophoresis [PFGE]), followed by characterization of selected isolates for genomic deletions that may be responsible for the lack of phase 2 flagellum expression.