Background: The primary cause of osteoporosis in women is increased bone resorption and decreased bone density associated with reduced estrogen secretion. Several studies have demonstrated a relationship between Helicobacter pylori infection and osteoporosis regardless of estrogen levels. This study examined the relationship between H. pylori infection and osteopenia together with estrogen levels, calcium intake, and several lifestyle factors. Methods: This study included 473 healthy women who underwent a general health examination. Multivariate analysis was performed, with age, body mass index (BMI), smoking habit, drinking habit, exercise habit, schooling duration, estradiol levels, birth history, calcium intake, schooling duration, smoking habit, drinking habit, exercise habit, and H. pylori infection as independent variables and the presence of osteopenia as a dependent variable. Results: The adjusted OR for osteopenia with H. pylori infection was 0.95 (95% CI 0.55-1.63, p = 0.84). In contrast, osteopenia was significantly associated with age, low BMI, lesser schooling period, low estradiol levels, and low calcium intake. Conclusions:H. pylori infection was not a significant risk for osteopenia by the multivariate analysis, which included the primary confounding factors. Significant factors, such as estradiol and calcium intake, should be assessed together to study the association of H. pylori infection and osteopenia.