To choose which treatment would be most effective for the individual patient with newly diagnosed achalasia is difficult for the tending physician. A diagnostic tool that would allow prediction of the symptomatic and functional response after treatment for achalasia is therefore needed. The timed barium esophagogram (TBE) is a method that allows objective assessment of esophageal emptying, but the value of TBE in the clinical management of achalasia remains to be clarified. The aim of this study was first, to assess the ability of TBE to predict symptoms and treatment failure during post-treatment follow-up. Second, to determine whether esophageal emptying as assessed by TBE differs after treatment with pneumatic dilatation or laparoscopic myotomy. Fifty-one patients with newly diagnosed achalasia were prospectively randomized to pneumatic dilatation (n = 26) or laparoscopic myotomy (n = 25). Evaluation with TBE was performed before (n = 46) and after treatment (n = 43). The median interval between treatment and post-treatment TBE was 6 months, and the median follow-up time after the post-treatment TBE was 18 months. Following therapeutic intervention, TBE parameters did not differ significantly between treatment groups. However, significant correlations were found between the height of the barium column at 1 min and the symptom scores at the end of follow up for 'dysphagia for liquids' (P < 0.05, rho = 0.47), 'chest pain' (P < 0.05, rho = 0.42), and the 'Watson dysphagia score' (P < 0.05, rho = 0.46). Patients with less than 50% improvement in this TBE-parameter (height at 1 min) post-treatment had a 40% risk of treatment failure during follow-up. In summary, pneumatic balloon dilatation and laparoscopic myotomy similarly affected esophageal function as assessed by TBE-emptying. Lack of improvement in barium-column height post-treatment was associated with an increased risk of treatment failure which should motivate close surveillance in order to detect symptomatic recurrence at an early stage.