A preoperative chest computed tomography examination of the right breast in a 52-year-old woman with breast cancer revealed multiple nodules in both lungs. The nodule in the apical segment of the upper lobe of the right lung was larger, at a diameter of approximately 2.1 cm. The patient underwent resection of the right breast, followed by thoracoscopic wedge resection of four pulmonary nodules. Hematoxylin and eosin staining and immunohistochemistry showed that the nodules in the apical and anterior segments of the upper lobe and the paravertebral nodule in the lower lobe of the right lung were primary adenocarcinoma, and the subpleural nodule in the lower lobe of the right lung was infiltrated with inflammatory cells. Exon sequencing was conducted in the resected tissue samples and blood specimens. According to the characteristics of the somatic mutations, the nodule in the apical segment of the upper lobe of the right lung was primary lung adenocarcinoma, the nodule in the anterior segment of the upper lobe and the paravertebral nodule in the lower lobe of the right lung were intrapulmonary metastatic cancer, and the subpleural nodule in the lower lobe of the right lung indicated early stage tumor progression. This case provides new evidence that conducting gene detection in multiple tissue samples from patients who have undergone resection may assist to determine the relationship among multiple nodules in the lung to exclude lung metastasis of breast cancer.