A coherent distinction between primary and secondary achalasia is considerably important to clinicians. This is because the therapeutic interventions for the two are entirely different. Whilst pneumatic dilation is the standard treatment in primary achalasia, the same treatment, if instituted in malignant stenosis carries potential risk to the patient and delays appropriate therapy of the underlying disorder. This distinction however, is extremely difficult. None of the available clinical, manometric, endoscopic or imaging criteria can reliably exclude secondary achalasia. However, suspicion may be raised and in such cases, an exhaustive work up including repeat biopsies and even surgery should be considered. In this review, we discuss the various problems in differentiating primary from secondary achalasia.