Background To compare the results of ultrasonic and Orbscan pachymetry in corneal haze not related to surgery. Methods An institutionally based, prospective, controlled clinical trial included 40 eyes of 40 consecutive patients with corneal haze not related to surgery. Fifty normal eyes were used as a control group to calculate the customized acoustic factor. Corneal haze was graded with slit-lamp by a single examiner. Ultrasonic and Orbscan II pachymetry measurements were obtained. Paired t- and Kruskal-Wallis tests were used to evaluate the difference between ultrasonic and Orbscan pachymetry measurements. Correlation of the two methods and haze grade were determined with Kendall's tau-b correlation analysis. Results Eighty-five percent of patients had moderate haze. With the customized acoustic factor, Orbscan values were significantly smaller than ultrasonic pachymetry measurements (p=0.001, paired samplet-test). Increased haze grade resulted in smaller Orbscan pachymetry measurements however, this difference was insignificant (p=0.444, Kruskal-Wallis test). A positive correlation was found between two methods, though insignificant (p=0.064, Kendall's tau-b correlation). When grouped in respect of diagnoses, differences in pachymetry measurements as well as the correlation were not significant (p > 0.05). Conclusions An insignificant positive correlation was found between the two methods in the presence of corneal haze. Orbscan measurements were inversely related to haze grading, and were significantly lower than ultrasonic pachymetry. According to our results, we recommend that clinicians should not count on Orbscan topography alone in the presence of corneal haze.