To study the effect of ocular inflammation in active uveitis on the corneal endothelium. This is a prospective cross-sectional study involving 63 eyes of 38 patients with active newly-diagnosed uveitis. Eighty-four eyes of 42 non-uveitic subjects served as a control group. All patients underwent detailed ophthalmic examination, laser flare photometry, and non-contact specular microscopy. Eyes with uveitis had a follow-up visit at one month after initiation of treatment, including laser flare photometry and specular microscopy. The mean age of the active uveitis patients was 33 (range: 9-67 years) with 21 men (55%) and 17 women (45%). For the uveitis patients at baseline, the mean flare value was 32ph/ms (range: 15-100ph/ms) with flare photometry value ≥50ph/ms in 13 eyes (21%) and<50ph/ms in 50 eyes (79%). At baseline, cell density (CD) of the uveitis patients was similar to CD in control eyes (p꞊0.16). The percent of hexagonality was significantly lower (p<0.0001), and the coefficient of variance (CV) (p<0.0001) and central corneal thickness (CCT) (p<0.0001) were significantly higher than in the control group. After one month, there was a significant decrease in flare photometry values (p<0.0001), with a mean flare value of 14.5ph/ms (range: 4-60ph/ms). In the active uveitis group, the overall results of specular microscopy did not significantly vary between the initial examination and the 1-month examination. For eyes with flare photometry value ≥50ph/ms at baseline, CD and hexagonal cell count significantly increased on the 1-month examination (p꞊0.01 and p꞊0.02 respectively), while CV and CCT decreased significantly at the one-month follow-up visit (p꞊0.007/p꞊0.03 respectively). For eyes with flare photometry value at baseline <50ph/ms, there was no significant differences in specular microscopy results between the initial examination and the 1-month examination. In eyes with newly-diagnosed uveitis and active anterior chamber inflammation, specular microscopy shows transient qualitative abnormalities of the corneal endothelium that depend on the severity of the anterior chamber inflammation as measured by the laser flare meter.