Association between periodontitis and cardiovascular disease can be explored by a various set of methods. Correlation between microflora in periodontitis and atherosclerosis has to be solved at the strain level. The choice of methods depends on lab facilities, and skilled hands. Combining different methods avoid false positive observations and verify accurate identifications. Serology reveals the host response as systemic versus local by analyzing body fluids for inflammation biomarkers and antibodies against invading pathogens at species level. Scanning electron microscopy (SEM) is useful to explore the localization and visualize the morphology of the microorganisms in the tissue. With the fluorescence in situ hybridization (FISH) technique, specific gene sequences can be explored in intact cells of the tissue sample and microorganisms can be differentiated at strain level. Proteomic analysis of the tissue sample reveals the active part of the infection, and detection of peptides that can be linked to specific microorganisms at strain level and host factors such as immune related factors. High through-put sequencing of total DNA from tissue samples reveals sequences from the tissue as well of microorganisms (metagenomics) but can be difficult to solve 100% because of lack of reference genomes of yet unidentified microorganisms when blasting those small sequence fragments. A sequence profile can be performed by cloning the 16S/18S PCR product or a genus-specific hybridization profiles by microarray hybridization. Whereas fingerprinting techniques based on pure bacteria or Candida make a specific fingerprinting pattern that can indicate strong correlation or not between samples from the same patient.