It is well known that there might be an epidemiological association between Helicobacter pylori infection and extraintestinal diseases. This study aimed at determining H. pylori infection in epileptic patients. Forty-seven cryptogenic epileptic patients (Group 1) and 35 healthy people (Group 2) participated in this study. Presence of H. pylori infection was examined by H. pylori stool antigen (HpSA), H. pylori IgG, and IgM. HpSA was detected in 21 participants (44.6%) in Group 1 and in 3 participants (8.5%) in Group 2. H. pylori IgM was positive in 27 participants (57.4%) in Group 1 and in 8 participants (22.8%) in Group 2. H. pylori IgG was positive in 37 participants (78.7%) in Group 1 and in 13 participants (38%) in Group 2. The difference of rates of HpSA, H. pylori IgM and IgG in Groups 1 and 2 were found statistically significant (χ2 = 4.18, p = 0.04; χ2 = 9.18, p = 0.0017; χ2 = 14.58, p < 0.001, respectively). We also compared presence of H. pylori infection between the epileptic patients with poor and good prognosis; HpSA positivity was detected in 15 (62.5%) of 24 and 6 (26%) of 23, respectively, and the differences were statistically significant (χ2 = 6.30, p = 0.012). H. pylori IgM positivity was detected in 16 (66%) of 24 patients with poor prognosis and 11 (47.8%) of 23 patients with good prognosis (p > 0.05). H. pylori IgG positivity was detected in 18 (75%) of 24 patients with poor prognosis and 19 (82.6%) of 23 patients with good prognosis. The differences of H. pylori IgM and IgG positivity rates in epileptic patients with poor and good prognosis were not found statistically significant (p > 0.05). These results suggest a probable association between the acute H. pylori infection and epilepsy, especially with poor prognosis.