The ocular microcirculation represents an important target to treat inflammatory diseases of eye, where impairment of microvascular blood flow plays key role as, for example, in anterior uveitis. To evaluate novel interventions targeting the microcirculation, appropriate and reliable tools to study this particular microvascular bed are needed. Intravital microscopy (IVM) belongs to several methods allowing evaluation of microcirculation experimentally, even in small animals. The aim of our study was to examine the iridial microcirculation (IMIC) in uveitis induced by local or systemic endotoxin administration in rats and mice by IVM and to propose new parameters to quantify the changes within the IMIC. Systemic inflammation was induced in rats by intravenous endotoxin administration, control group received normal saline intravenously. Local inflammation was induced in mice by intravitreal endotoxin administration, the control group received normal saline intravitreally. IVM of IMIC was performed in animals receiving systemic endotoxin prior injection and 1 and 2 h afterwards, respectively, in animals receiving intravitreal endotoxin/saline prior local injection and 5 h afterwards. Obtained video recordings were analyzed off-line. Functional capillary density (FCD) and dysfunctional capillary density (DCD) were evaluated for description of IMIC, and calculation of FCD/DCD ratio was performed. In systemic inflammation, FCD was significantly decreased compared to control animals. In local inflammation, the number of functional capillaries in the IMIC was significantly reduced following the endotoxin challenge. Analysis of the DCD revealed a significant increase in capillaries with reduced perfusion after intravitreal endotoxin administration and right shift of the FCD/DCD ratio was observed after endotoxin local injection. Detecting and quantifying changes in IMIC during systemic or local inflammation in experimental animals by IVM was feasible. Therefore, IVM of the IMIC represents a valuable tool to evaluate and quantify inflammatory changes in experimental eye disease.