Immunohistochemical assessment of programmed cell death (PD)-ligand 1 (PD-L1) expression in lung cancer in the context of therapeutically targeting the PD1/PD-L1 axis is still controversially discussed. This includes the comparability of antibody clones, prognostic value, and discrepancies between primary tumors and metastases. We assessed tumoral PD-L1 expression using clones E1L3N and SP142 in 372 primary resected pulmonary squamous cell carcinomas, including 40 paired N2 lymph node metastases, in relation with clinico-pathological parameters. PD-L1 expression was negative (<1%) in 163/372 (44%, E1L3N) or 231/370 patients (62%, SP142). Positivity of 1-<50% was observed in 135 (36%, E1L3N) or 92 patients (25%, SP142) and ≥50% in 74 (20%, E1L3N) or 47 patients (13%, SP142). PD-L1 staining correlated significantly between both antibodies (r=0.781; P<0.001). Scores correlated significantly between full-slide sections (N=40) and tissue microarrays, and between primaries and N2 metastases (P<0.001 all). CD8+ tumor infiltrating lymphocyte counts positively correlated with PD-L1 expression (P<0.001). PD-L1 ≥50% showed the best prognostic discrimination using the split-sample validation method. It was associated with shorter disease-specific survival in the observation group (E1L3N: P=0.035, SP142: P=0.002) and validation group (E1L3N: P=0.024, SP142: P=0.101) and shorter time to recurrence (observation group: E1L3N: P=0.056, SP142: P<0.001; validation group: E1L3N: P=0.036, SP142: P=0.247). Multivariate analysis showed that PD-L1 expression ≥50% determined by clone E1L3N was an independent prognostic factor in the observation group regarding disease-specific survival (HR=2.768; 95% CI=1.149-6.666; P=0.023) and time to recurrence (HR=2.164; 95% CI=1.056-4.436; P=0.035) and in the validation group (disease-specific survival: HR=1.978; 95% CI=0.928-4.214; P=0.077 and time to recurrence: HR=1.571; 95% CI=0.838-2.944; P=0.159). High PD-L1 expression was associated with adverse prognosis in pulmonary squamous cell carcinoma. Clone E1L3N was more sensitive than SP142 and superior regarding prognostication. PD-L1 expression correlated significantly between primary tumor and N2 metastases, rendering mediastinal lymph node metastases adequate for immunohistochemical assessment.