The aim of this study was to assess the quantity of interstitial cells of Cajal (ICC) in the lower esophageal sphincter (LES) in achalasia. LES muscle was obtained from 11 achalasia and nine esophageal cancer (control) patients during surgery. Immunohistochemistry was performed and average cell counts per high-power field (HPF) were obtained. Overall, more ICC were observed in achalasia (median = 14.0 cells/HPF; range = 0–22.6 cells/ HPF) as compared with controls (median = 6.2 cells/HPF; range = 1.6–10.8 cells/HPF) (P= 0.047). There were two subsets of findings within the achalasia group: 8/11(73%) had an increased quantity of ICC (median =17.1 cells/ HPF; range = 11.6–22.6; P = 0.015) as compared with controls, whereas the remaining 3/11(27%) had a paucity of ICC (median = 0 cells/HPF; range = 0–2; P = 0.02). ICC levels were positively correlated with age of the patient (P= 0.043). Our study demonstrates that subsets of abnormal ICC levels are observed in idiopathic achalasia of the esophagus.