Abdominal aortic aneurysm (AAA) and peripheral artery disease (PAD) share pathophysiological mechanisms including the activation of the fibrinolytic and innate immune system, which explains the analysis of D-dimer and myeloperoxidase (MPO) in both conditions. This study evaluates the diagnostic marker potential of both variables separately and as a combined MPO/D-dimer score for identifying patients with AAA versus healthy individuals or patients with PAD. Plasma levels of MPO and D-dimer were increased in PAD and AAA compared to healthy controls (median for MPO: 13.63 ng/mL [AAA] vs. 11.74 ng/mL [PAD] vs. 9.16 ng/mL [healthy], D-dimer: 1.27 μg/mL [AAA] vs. 0.58 μg/mL [PAD] vs. 0.38 μg/mL [healthy]). The combined MPO/D-dimer score (median 1.26 [AAA] vs. −0.19 [PAD] vs. −0.93 [healthy]) showed an improved performance in distinguishing AAA from PAD when analysed using the receiver operating characteristic curve (area under the curve) for AAA against the pooled data of healthy controls + PAD: 0.728 [MPO], 0.749 [D-dimer], 0.801 [score]. Diagnostic sensitivity and specificity ranged at 82.9% and 70.2% (for score cut-off = 0). These findings were confirmed for a separate collective of AAA patients with 35% simultaneous PAD. Thus, evaluating MPO together with D-dimer in a simple score may be useful for diagnostic detection and the distinction of AAA from athero-occlusive diseases like PAD.