Abstract—Objective: Atrial fibrillation (AF) is a common cause of cerebral infarction resulting from thromboembolism. The left atrial appendage (LAA) is the main location of thrombus formation. The objective of this study is to quantify the morphological structure of pectinate muscle inside LAA using fractal analysis. Methods: In this study, fractal analysis of pectinate muscle consists of two steps. The first step was image segmentation using the region growing method based on grayscale to extract the border of LAA. Then the fractal dimension (FD) of the border of LAA was calculated using box-counting method. This quantitative analysis was assessed via both healthy volunteers (n=7, age: 61±5, male, 5) and thrombus patients (n=3, age: 63±6, male, 2). Mann Whitney U test was used for statistical analysis. Results: For image segmentation, the region growing method successfully segmented the borders of LAA for all volunteers and patients. The FD values of healthy groups and thrombus groups were 1.179±0.005 and 1.113±0.006, respectively. The mean FD value of healthy groups was higher than in thrombus groups (p < 0.0001). Conclusion: Fractal analysis provides an effective measurement to quantify the complexity of pectinate muscle inside LAA and has the potential to distinguish thrombus patients from health.