Objective: Lack of the adhesion molecule CD44 reduces collateral artery growth (arteriogenesis) in a murine hindlimb model. CD44 function is influenced by expression of 10 alternatively spliced exons (v1-v10), with unknown effects on arteriogenesis. As the variant exon CD44v3 binds heparan sulphate and facilitates preservation of growth factors, we hypothesized that the variably spliced exon region of CD44, especially exon CD44v3, is involved in arteriogenesis. Materials and Methods: The right femoral artery of C57BL/6J-mice was ligated and tissue was processed for histological and qPCR analysis of CD44-isoform expression. Microsphere perfusion measurements were performed in mice lacking the variably spliced exon region (CD44s knock-in mice), and in knock-in strains with specific isoform expression (CD44v3-10 and CD44v4-10), as well as in double knock-in mice, expressing CD44v3-10 and CD44s. Results: Expression of total CD44 and CD44v3 mRNA following femoral artery ligation was increased, accompanied by increased mRNA levels of the CD44-relevant splicing factors Tra2-beta1 and SRm160. CD44v3-expression was limited to the vessel wall of growing collateral arteries. Perfusion restoration was significantly reduced in mice lacking the variably spliced exon region (CD44s):20.1±1.3%, compared to the background strain: 57.3±2.2%. Mice expressing exon v3 (CD44v3-10) showed perfusion percentages of 25.9±1.1%, compared to mice lacking this exon (CD44v4-10):19.1±0.7%. Combined expression of CD44v3 and CD44s further improved perfusion restoration: 33.1±2.6%. Conclusion: Total CD44 and CD44v3 mRNA are upregulated during arteriogenesis. The absence of the variably spliced exon region impairs arteriogenesis. Presence of exon v3 of CD44 results in improved arteriogenesis. Expression of CD44s and CD44v3 provides a synergistic effect on arteriogenesis. As this combined expression still resulted in hampered arteriogenesis, a specific role of exon v2 in arteriogenesis appears likely.