The improvement of learning quality might be pursued by improving the learning process based on the results of diagnosing the students’ learning difficulties. The study then was to diagnose the junior high school students’ learning difficulties in completing the mathematics test items of the national examination. The study is a quantitative descriptive study. The diagnosis of learning difficulties was conducted by performing the cognitive diagnostic assessment through using DINA model. The data that had been used in the study were students’ responses of math test of national examination of junior high schools located in the Province of Yogyakarta Special Region, Indonesia. The students’ difficulties were detected by implementing the CDM package provided by the R program and using the output of the latent classes were identified. The results of the study showed that the students experienced some difficulties in completing the national examination test in many items on number, geometry and statistics, and understanding the narrative text items.