Background: Gastroesophageal reflux disease (GERD) is a common disorder. The aim of our study was to describe the prevalence of nighttime heartburn and its associations with esophagitis, Barrett’s esophagus, and extra-esophageal symptoms. Methods: Data were collected as part of the ongoing Progression of Gastroesophageal Reflux Disease (ProGERD) study. Based on endoscopy results, patients were categorized as having nonerosive GERD, erosive GERD, or Barrett’s esophagus. ORs and 95% CIs derived from logistic regression analysis were calculated for the association between nighttime heartburn and GERD complications. Results: The overall prevalence of nighttime heartburn for at least 1 of 3 years was 49%, and 21% of patients reported nighttime heartburn in all 3 years. According to multivariate analysis, chronic nighttime heartburn was associated with globus sensation (OR 1.79, 95% CI 1.29–2.47) and erosive GERD (OR 1.67, 95% CI 1.29–2.15). Compared to continuous proton pump inhibitor (PPI) intake, noncontinuous PPI therapy (OR 2.26, 95% CI 1.73–2.96) and medication other than PPIs (OR 2.46, 95% CI 1.67–3.62) were also associated with chronic nighttime heartburn. Conclusions: The prevalence of nighttime heartburn in GERD patients under routine care was high, even in patients on continuous PPI therapy. Nighttime heartburn was not associated with Barrett’s esophagus or most extra-esophageal symptoms.