Technical Abstract: Analysis of the complete genomic sequence of Campylobacter jejuni strain RM1221 identified four large genomic elements, Campylobacter jejuni integrated elements (CJIEs), that were absent from C. jejuni strain NCTC 11168. To further investigate the genomic diversity of Campylobacter, we conducted a comparative genomic analysis from a collection of 67 C. jejuni and 12 Campylobacter coli strains isolated from various geographical locations and clinical and veterinary sources. Utilizing PCR, we demonstrated that 55% of the C. jejuni strains examined were positive for at least one RM1221-like genomic element, and 27% were positive for two or more of these CJIEs. Furthermore, 58% of C. coli strains were positive for either genomic elements CJIE1 or CJIE 3. To simultaneously assess for the presence or absence of several genes that comprise the various CJIEs, we developed a multi-strain C. jejuni DNA microarray that contained most of the putative coding sequences for strains NCTC 11168 and RM1221. A comparative genomic indexing analysis of 35 C. jejuni strains confirmed the presence of genomic elements similar to those in strain RM1221. Interestingly, the DNA microarray analysis demonstrated that these genomic elements in the other C. jejuni strains often exhibited modular patterns with some regions present and other regions either absent or highly divergent as compared to strain RM1221. We also showed that in CJIE1, a Campylobacter Mu-like phage, is located differentially in other isolates of C. jejuni. Our DNA microarray specifically identified 14 regions in strain RM1221 that were distinct from strain NCTC 11168, such as the capsule and lipooligosaccharide biosynthesis regions. This study extends our knowledge of the known hypervariable regions described in previous comparative genomic analyses of C. jejuni. Thus, the inclusion of these integrated genomic elements, initially identified in strain RM1221, contributes to a better assessment of the diversity in C. jejuni and may increase the usefulness of DNA microarrays as an epidemiological genotyping tool.