In this paper, we introduce the Protocol Genome, a self-supervised learning system that learns correlations from DICOM headers and achieves AUROC 0.901 (vs 0.847 baseline) and ECE 0.036 (vs 0.058) on fully held-out external validation. Our method also improves calibration and robustness across modalities (CT, MRI, CXR) and vendors. Clinical imaging is funneled through PACS/DICOM, where procedure choices (scanner make/model, sequence, kernel, kVp, TR/TE, and slice thickness) have consequences for contrast, noise, and artifact. These latent confounders impede the generalization of image-only networks across sites. We consider structured DICOM headers as a label and learn protocol-aware but clinically robust image representations. Protocol Genome obtains tokenized embeddings of de-identified header fields and models them along with image features using: (1) protocol-image contrastive learning, (2) masked protocol prediction, and (3) protocol-protocol translation. With 1.26M studies (7 health systems, 31 scanners, 3 vendors; CT, MR, CR/DR), we experiment on: (A) chest CT triage for PE, (B) brain MRI glioma grading, and (C) chest radiograph cardiomegaly detection. Relative to strong SSL baselines (SimCLR, MAE) as well as ImageNet transfer, Protocol Genome (+0.046: PE, +0.058: glioma, +0.041: cardiomegaly) is associated with higher external AUROC; 25-37% calibration improvements are obtained (p < 0.01, DeLong tests). While the gains may be task-dependent, they are preserved with 10-20% of labeled data. From a clinical point of view, the technique reduces false positives at protocol borders and is applicable in a PACS (DICOM C-FIND/C-MOVE, DICOMweb QIDO/WADO). We publish a model card and deployment guide, complete with both de-identification and bias audits.