Wireless capsule endoscopy (WCE) has revolutionised the diagnosis and treatment of gastrointestinal tract, especially the small intestine which is unreachable by traditional endoscopies. The drawback of the WCE is that it produces a large number of images to be inspected by the clinicians. Hence, the design of a computer‐aided diagnosis (CAD) system will have a great potential to help reduce the diagnosis time and improve the detection accuracy. To address this problem, the authors propose a CAD system for automatic detection of ulcer in WCE images. Firstly, they enhance the input images to be better exploited in the main steps of the proposed method. Afterward, segmentation using saliency map‐based texture and colour is applied to the WCE images in order to highlight ulcerous regions. Then, inspired by the existing feature extraction approaches, a new one has been proposed for the recognition of the segmented regions. Finally, a new recognition scheme is proposed based on hidden Markov model using the classification scores of the conventional methods (support vector machine, multilayer perceptron and random forest) as observations. Experimental results with two different datasets show that the proposed method gives promising results.