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We study the effect of clustering on the organization of cooperation by analyzing the evolutionary dynamics of the “Prisoner’s Dilemma” on scale-free networks with a tunable value of clustering. We find, on the one hand, that a high value of the clustering coefficient produces an overall enhancement of cooperation in the network, even for a very high temptation to defect. On the other hand, high clustering homogenizes the process of invasion of degree classes by defectors, decreasing the chances of survival of low densities of cooperators in the network.