Background: There is inconclusive evidence to suggest the expression of programmed cell death (PD) ligand 1 (PD-L1) is a putative predictor of response to PD-1/PD-L1 targeted therapies in LC. We evaluated the heterogeneity in the expression of PD-1 and its ligands in isogeneic primary and metastatic LC specimens from 12.580 post mortem samples. Methods: We identified 214 patients with untreated metastatic LC, of which 98 had adequately preserved tissues to construct a syngeneic primary LC/metastasis tissue microarray. Immunostaining for PD-1, PD-L1 & 2 was evaluated in primary and metastatic lesions and correlated with patient demographics, tumour histology and pattern of metastatic spread. Results: 98 patients with a median age of 70 years, 77 (75%) with Stage IV disease were included. Non-small cell LC (NSCLC) cases (n = 65, 66%) included 32 adenocarcinomas, 30 squamous cell and 3 mixed carcinomas. 29 (30%) extensive-stage SCLC and 4 (4%) atypical carcinoids (AC) were included. No staining for PD-1 was detected in the peritumoral stroma. In total, 8/65 (12%) primary NSCLC were PD-L1 positive, with the majority of matched metastases (14/17, 82%) being PD-L1 negative. SCLCs were universally PD-L1 negative across primary and metastatic disease. We found PD-L2 immunostaining in 11/65 NSCLC (17%), 2/29 SCLC (7%) and 1/4 AC (25%). Only 2/30 (7%) of matched metastatic deposits were PD-L2 positive. We found no correlation between the expression of PD ligands and stage, however PD-L2 expressing primaries had more frequently metastasized to the kidneys (43% versus 11%, p = 0.003). Conclusions: Intratumor heterogeneity in the expression of PD ligands is common in NSCLC, whilst PD-L1 is homogeneously undetectable in primary and metastatic SCLC. This holds implications in the clinical development of immune response biomarkers in LC.