Abstract: Background: The purpose of this study was to evaluate the difference between oral aphthae in Behcet’s Disease (BD) and recurrent aphthous stomatitis (RAS). Methods: In a prospective study 56 cases of BD and 133 RAS were evaluated consecutively. Sex, age of onset, frequency of aphthous lesions, their duration and their mean number at each attack, pathergy test, HLA-B5, HLA-B51 and HLA-B27 were evaluated in both groups. Comparison was made by Student t test and chi2 test. Results: The mean age in BD group was 33.9 years (SD=9, CI=2.4), while in the RAS group it was 31.4 years (SD=9.2, CI=1.6), t was 0.994 (p=0.32). Mean time from the onset: BD 5.9 years (SD=6.3, CI=1.6), RAS 6.4 (SD=6.7, CI=1.2), t=0.450, p=0.65. Frequency of attacks: BD 28 days (SD=29.7, CI=8), RAS 36 (SD=35, CI=6.1), t=1.315, p=0.19. Mean number of ulcers: BD 3.6 (SD=2.3, CI=0.6), RAS 3.1 (SD=2.1, CI=0.4), t=1.514, p=0.13. Mean duration of attacks: BD 9.5 days (SD=5.3, CI=1.4), RAS 10 (SD=4.93, CI=0.7), t=0.669, p=0.50. Sex: BD male 63% (CI=12.6), RAS male 49% (CI=8.5), chi2=2.937, p=0.09. HLA-B5: BD 64% (CI=12.6), RAS positive 22.6% (CI=7.2), chi2=30.195, p<0.0001. HLA-B51: BD 37.5% (CI=12.6), RAS 18% (CI=6.5), chi2=8.222, p=0.004. HLA-B27: BD 9% (CI=7.5), RAS 2.3% (CI=2.4), Chi2=2.839, p=0.09. Pathergy test: BD 57% (CI=13), RAS: 5% (CI=3.7), chi2=63.640,p<0.0001. Conclusions: There was no significant difference between BD and RAS regarding sex, age of onset, number of attacks, number and the duration of the ulcers. There was a significant difference in positive pathergy test, HLA-B5, and HLA-B51.