Helicobacter pylori (H.pylori) is the primary cause of gastric cancer and eradication in healthy adults has proven effective in decreasing cancer incidence. H.pylori is acquired largely in early childhood, however, the benefits of eradication in children are controversial. We aimed to determine the effect of H.pylori eradication on clinical and laboratory markers associated with gastric damage in apparently healthy school-aged children. This was a pilot non-blinded trial including 61 children persistently infected with H.pylori who were randomized to eradication/no treatment and followed for at least 12months, evaluating clinical and blood markers (Pepsinogen I (PGI) and II (PGII) determined by ELISA) associated with gastric damage. The treatment consisted of a sequential scheme including 7days of omeprazole+amoxicillin followed by 7days of omeprazole+clarithromycin+metronidazole; adherence and tolerance were surveyed. Eradication rates were assessed by stool antigen detection or urea breath test 1month following treatment every 4months thereafter to detect reinfection. Eradication occurred in 30/31 treated children (median age: 8.8, range: 7.9-10.8) and in 0/30 non-treated controls (median age: 8.6, range: 7.9-11) (p<.001). Treatment was associated with mild transient symptoms (altered taste, nocturnal upper abdominal pain, nausea, and diarrhea). Baseline frequency of symptoms was low and eradication did not change symptoms compared to controls. PGI, PGII, and anti-H.pylori seropositivity were similar in both groups at baseline and significantly decreased only in eradicated patients; PGI (92.5 vs. 74.4, p<.001), PGII (15.2 vs. 8.9, p<.001) levels, and frequency of anti-H.pylori seropositivity (100 vs. 68%, p<.001) respectively. Four eradicated children (13%) were reinfected during follow-up. H.pylori eradication therapy in apparently asymptomatic school-aged children was well tolerated and associated with decreased serum PGI and PGII levels. Future studies should expand on the middle-long-term effect of early H.pylori eradication, especially on preventing gastric cancer.