The purpose of this study was to evaluate the prognostic value of L-type amino acid transporter 1 (LAT 1) and 4F2 heavy chain (CD98) in patients with stage I squamous cell carcinoma of the lung. A total of 84 consecutive patients with completely resected pathologic stage I squamous cell carcinoma of the lung were retrospectively reviewed. All patients underwent resection of the tumor and the immunohistochemical analysis was done to determine the expression of LAT 1, CD98, Ki-67 labeling index, vascular endothelial growth factor, and microvessel density. These pathological parameters were correlated with the prognosis of patients after complete resection of the tumor. A positive rate of LAT 1 expression (87%; 73/84) was significantly higher than that of CD98 expression (65%; 55/84) (P = 0.0018). Cooperative expression of LAT 1 and CD98 was recognized in 62% (52/84). LAT 1 expression was significantly correlated with CD98, Ki-67 labeling index, vascular endothelial growth factor, and microvessel density. The 5-year survival rates of the LAT 1-positive and LAT1-negative patients were 59% and 88%, respectively (P = 0.2186). Tumor cell proliferation and angiogenesis were not also (a) prognostic factor. However, the 5-year survival rate of patients with both LAT 1 and CD98-positivity (57%) was significantly worse than that of other patients (88%; P = 0.0136). Multivariate analysis confirmed that positive cooperative expression of LAT 1 and CD98 was an independent factor for predicting a poor prognosis. A cooperative expression of LAT 1 and CD98 is a significant pathological factor for predicting the poor prognosis in patients with resectable stage I squamous cell carcinoma of the lung.